Basic R question
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nac ▴ 280
@nac-4545
Last seen 10.3 years ago
HI , I want to subset a list I have in order to look only the data from chosen chromosomes. my file is this format ( see attached for a workable example) . This dataframe contain 6 columns, ID (X10th.txt., X11th.txt..), chrom(1---X,Y), loc.start and loc.end( coordinate), num.mark and seg mean. I would like to create the same file ( with 6 columns) but only containing information from chromosome 1, then another one for 2 then 3...Y. Could somebody help please? > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] cghMCR_1.8.0 limma_3.4.3 CNTools_1.6.0 genefilter_1.32.0 [5] DNAcopy_1.24.0 loaded via a namespace (and not attached): [1] annotate_1.26.0 AnnotationDbi_1.10.1 Biobase_2.8.0 [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.11.1 [7] survival_2.35-8 xtable_1.5-6 thanks a lot Nathalie ID chrom loc.start loc.end num.mark seg.mean 1 X10Th.txt 1 3002738 4.2E+07 3202 -0.0163 2 X10Th.txt 1 4.2E+07 4.2E+07 2 -0.7027 3 X10Th.txt 1 4.2E+07 1.7E+08 10731 0.0081 4 X10Th.txt 1 1.7E+08 1.7E+08 11 0.7461 5 X10Th.txt 1 1.7E+08 2.0E+08 2448 -0.0052 6 X10Th.txt 10 3002742 1.3E+08 11833 -0.0574 7 X10Th.txt 11 3026911 3100146 12 -0.4499 8 X10Th.txt 11 3102021 3.4E+07 2516 0.007 9 X10Th.txt 11 3.4E+07 3.4E+07 4 0.7885 10 X10Th.txt 11 3.4E+07 7.1E+07 3834 -0.0119 11 X10Th.txt 11 7.1E+07 7.1E+07 10 -1.5455 12 X10Th.txt 11 7.1E+07 8.3E+07 1618 0.0099 13 X10Th.txt 11 8.3E+07 8.4E+07 2 -1.9797 14 X10Th.txt 11 8.4E+07 9.0E+07 739 0.0197 15 X10Th.txt 11 9.0E+07 9.0E+07 3 0.4815 16 X10Th.txt 11 9.0E+07 1.2E+08 3920 -0.0171 17 X10Th.txt 12 3095298 6.3E+07 4424 0.0474 18 X10Th.txt 12 6.3E+07 6.3E+07 3 0.5165 19 X10Th.txt 12 6.3E+07 1.1E+08 5209 0.0385 20 X10Th.txt 12 1.1E+08 1.1E+08 6 -0.4526 21 X10Th.txt 12 1.1E+08 1.2E+08 201 0.1305 22 X10Th.txt 12 1.2E+08 1.2E+08 19 0.614 23 X10Th.txt 12 1.2E+08 1.2E+08 481 0.0334 24 X10Th.txt 13 3004789 1.2E+08 10642 -0.3045 25 X10Th.txt 14 3892581 5.2E+07 4281 0.5563 26 X10Th.txt 14 5.2E+07 5.2E+07 4 -0.4408 27 X10Th.txt 14 5.2E+07 5.2E+07 11 -1.4074 28 X10Th.txt 14 5.2E+07 5.3E+07 12 -0.6649 29 X10Th.txt 14 5.3E+07 5.3E+07 18 -1.5591 30 X10Th.txt 14 5.3E+07 5.3E+07 56 -2.6024 31 X10Th.txt 14 5.3E+07 6.8E+07 1815 0.5608 32 X10Th.txt 14 6.8E+07 6.8E+07 33 0.1478 33 X10Th.txt 14 6.8E+07 1.2E+08 4457 0.5724 34 X10Th.txt 15 3091692 3.9E+07 2821 0.6079 35 X10Th.txt 15 3.9E+07 3.9E+07 5 0.1051 36 X10Th.txt 15 3.9E+07 3.9E+07 12 0.5436 37 X10Th.txt 15 3.9E+07 3.9E+07 2 -0.8667 38 X10Th.txt 15 3.9E+07 1.0E+08 6464 0.6688 39 X10Th.txt 16 3151162 6024268 339 -0.1676 40 X10Th.txt 16 6032525 6045766 3 -2.3133 41 X10Th.txt 16 6056091 3.6E+07 3366 -0.136 42 X10Th.txt 16 3.6E+07 3.6E+07 4 -1.392 43 X10Th.txt 16 3.6E+07 9.8E+07 5329 -0.1383 44 X10Th.txt 17 3009074 9.5E+07 9007 -0.1542 45 X10Th.txt 18 3181133 9.1E+07 8058 -0.0622 46 X10Th.txt 19 3147156 1.7E+07 1848 -0.3487 47 X10Th.txt 19 1.7E+07 1.8E+07 100 -0.9124 48 X10Th.txt 19 1.8E+07 6.1E+07 4443 -0.3708 49 X10Th.txt 2 3010301 3.1E+07 2777 0.1381 50 X10Th.txt 2 3.1E+07 3.1E+07 4 -0.3156 51 X10Th.txt 2 3.1E+07 7.2E+07 3546 0.1484 52 X10Th.txt 2 7.2E+07 7.2E+07 2 -0.4492 53 X10Th.txt 2 7.2E+07 9.0E+07 1994 0.1389 54 X10Th.txt 2 9.0E+07 9.0E+07 2 0.7181 55 X10Th.txt 2 9.0E+07 9.1E+07 192 0.1815 56 X10Th.txt 2 9.1E+07 9.1E+07 4 0.6128 57 X10Th.txt 2 9.1E+07 1.8E+08 8335 0.1312 58 X10Th.txt 3 3007185 1.4E+08 11302 -0.1118 59 X10Th.txt 3 1.4E+08 1.4E+08 3 1.1729 60 X10Th.txt 3 1.4E+08 1.6E+08 1828 -0.1205 61 X10Th.txt 4 3012291 3335299 10 0.0708 62 X10Th.txt 4 3353037 9459467 498 0.6502 63 X10Th.txt 4 9469402 9469402 3 -0.1167 64 X10Th.txt 4 9473906 1.1E+07 123 0.8942 65 X10Th.txt 4 1.1E+07 1.4E+07 253 0.334 66 X10Th.txt 4 1.5E+07 1.6E+07 150 0.8265 67 X10Th.txt 4 1.6E+07 1.9E+07 179 0.322 68 X10Th.txt 4 1.9E+07 2.5E+07 463 0.8283 69 X10Th.txt 4 2.5E+07 2.5E+07 2 -4.1559 70 X10Th.txt 4 2.5E+07 3.7E+07 759 0.8149 71 X10Th.txt 4 3.7E+07 3.7E+07 20 1.2765 72 X10Th.txt 4 3.7E+07 5.9E+07 1833 0.4829 73 X10Th.txt 4 5.9E+07 6E+07 83 1.0287 74 X10Th.txt 4 6.0E+07 6.6E+07 455 0.623 75 X10Th.txt 4 6.6E+07 6.6E+07 3 -4.8121 76 X10Th.txt 4 6.6E+07 8.7E+07 1509 0.4519 77 X10Th.txt 4 8.7E+07 8.8E+07 37 0.9291 78 X10Th.txt 4 8.8E+07 9.7E+07 764 0.3171 79 X10Th.txt 4 9.7E+07 1.0E+08 417 0.8177 80 X10Th.txt 4 1.0E+08 1.0E+08 35 1.3066 81 X10Th.txt 4 1.0E+08 1.1E+08 1125 0.7607 82 X10Th.txt 4 1.1E+08 1.2E+08 933 0.3508 83 X10Th.txt 4 1.2E+08 1.2E+08 192 0.8091 84 X10Th.txt 4 1.2E+08 1.2E+08 15 1.3286 85 X10Th.txt 4 1.2E+08 1.2E+08 78 0.8328 86 X10Th.txt 4 1.2E+08 1.4E+08 1514 0.3228 87 X10Th.txt 4 1.4E+08 1.4E+08 3 1.2655 88 X10Th.txt 4 1.4E+08 1.5E+08 1352 0.283 89 X10Th.txt 4 1.5E+08 1.5E+08 41 0.8091 90 X10Th.txt 4 1.5E+08 1.6E+08 793 0.2844 91 X10Th.txt 5 3003879 3.3E+07 2707 0.105 92 X10Th.txt 5 3.3E+07 3.3E+07 3 -0.6753 93 X10Th.txt 5 3.3E+07 9.4E+07 5039 0.1072 94 X10Th.txt 5 9.4E+07 9.6E+07 8 -0.8031 95 X10Th.txt 5 9.6E+07 1.5E+08 6236 0.1028 96 X10Th.txt 6 3024849 2.6E+07 1843 -0.1733 97 X10Th.txt 6 2.6E+07 2.6E+07 2 -0.773 98 X10Th.txt 6 2.6E+07 3.4E+07 864 -0.1393 99 X10Th.txt 6 3.4E+07 3.4E+07 3 -2.5977 100 X10Th.txt 6 3.4E+07 4.1E+07 744 -0.1363 101 X10Th.txt 6 4.1E+07 4.1E+07 60 -0.9053 102 X10Th.txt 6 4.1E+07 1.2E+08 7693 -0.1561 103 X10Th.txt 6 1.2E+08 1.2E+08 2 0.5483 104 X10Th.txt 6 1.2E+08 1.5E+08 2924 -0.1333 105 X10Th.txt 7 3049177 2.9E+07 2215 -0.174 106 X10Th.txt 7 2.9E+07 2.9E+07 3 -0.8632 107 X10Th.txt 7 2.9E+07 3.4E+07 496 -0.1613 108 X10Th.txt 7 3.4E+07 3.5E+07 55 -0.6911 109 X10Th.txt 7 3.5E+07 1.0E+08 6236 -0.1745 110 X10Th.txt 7 1.0E+08 1.0E+08 5 -1.4229 111 X10Th.txt 7 1.0E+08 1.0E+08 20 -0.1964 112 X10Th.txt 7 1.0E+08 1.0E+08 6 -1.8286 113 X10Th.txt 7 1.0E+08 1.5E+08 4582 -0.1627 114 X10Th.txt 8 3111085 1.3E+08 11524 -0.1437 115 X10Th.txt 9 3088282 1.2E+08 12045 0.2501 116 X10Th.txt X 3086068 1.7E+08 12085 -0.0107 117 X10Th.txt Y 27 263780 52 -1.2383 118 X10Th.txt Y 263932 631098 15 -0.5181 119 X10Th.txt Y 631698 2177516 532 -1.256 120 X11Th.txt 1 3002738 2.0E+08 16394 -0.046 121 X11Th.txt 10 3002742 2.2E+07 1710 -0.2582 122 X11Th.txt 10 2.2E+07 2.2E+07 2 -2.3611 123 X11Th.txt 10 2.2E+07 1.3E+08 10121 -0.2586 124 X11Th.txt 11 3026911 3.4E+07 2528 -0.049 125 X11Th.txt 11 3.4E+07 3.4E+07 5 1.0058 126 X11Th.txt 11 3.4E+07 1.2E+08 10125 -0.035 127 X11Th.txt 12 3095298 6.3E+07 4424 -0.0904 128 X11Th.txt 12 6.3E+07 6.3E+07 3 1.7028 129 X11Th.txt 12 6.3E+07 1.2E+08 5916 -0.0654 130 X11Th.txt 13 3004789 1.3E+07 854 -0.1304 131 X11Th.txt 13 1.3E+07 1.3E+07 5 -1.3861 132 X11Th.txt 13 1.3E+07 2.8E+07 1591 -0.1782 133 X11Th.txt 13 2.8E+07 2.8E+07 5 -1.3185 134 X11Th.txt 13 2.8E+07 6.5E+07 3634 -0.1527 135 X11Th.txt 13 6.6E+07 6.7E+07 8 -1.1874 136 X11Th.txt 13 6.7E+07 6.9E+07 201 -0.1626 137 X11Th.txt 13 6.9E+07 6.9E+07 4 1.0844 138 X11Th.txt 13 6.9E+07 1.2E+08 4340 -0.1625 139 X11Th.txt 14 3892581 5.3E+07 4319 0.6606 140 X11Th.txt 14 5.3E+07 5.3E+07 58 -1.4906 141 X11Th.txt 14 5.3E+07 1.2E+08 6310 0.6554 142 X11Th.txt 15 3091692 8039326 448 0.4734 143 X11Th.txt 15 8040778 8040778 3 1.6185 144 X11Th.txt 15 8046698 3.9E+07 2358 0.454 145 X11Th.txt 15 3.9E+07 3.9E+07 3 1.5325 146 X11Th.txt 15 3.9E+07 1.0E+08 6492 0.4605 147 X11Th.txt 16 3151162 9.8E+07 9041 -0.2314 148 X11Th.txt 17 3009074 9.5E+07 9007 -0.0573 149 X11Th.txt 18 3181133 9.1E+07 8058 0.0341 150 X11Th.txt 19 3147156 6.1E+07 6391 -0.1194 151 X11Th.txt 2 3010301 5.0E+07 4560 0.1442 152 X11Th.txt 2 5.0E+07 5.0E+07 4 1.1306 153 X11Th.txt 2 5.0E+07 1.8E+08 12292 0.1487 154 X11Th.txt 3 3007185 6032558 245 -0.2823 155 X11Th.txt 3 6056822 6072724 3 1.2882 156 X11Th.txt 3 6083291 1.6E+08 12885 -0.2812 157 X11Th.txt 4 3012291 3146483 5 -0.8101 158 X11Th.txt 4 3159538 1.6E+08 13637 0.2846 159 X11Th.txt 5 3003879 1.1E+07 656 0.0416 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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Brian Herb ▴ 80
@brian-herb-3002
Last seen 10.3 years ago
Nathalie- try- chr1=subset(object,object$chrom==1) where object is your dataframe On Thu, Jul 14, 2011 at 10:34 AM, Nathalie Conte <nac@sanger.ac.uk> wrote: > HI , > I want to subset a list I have in order to look only the data from chosen > chromosomes. > my file is this format ( see attached for a workable example) . This > dataframe contain 6 columns, ID (X10th.txt., X11th.txt..), chrom(1 ---X,Y), > loc.start and loc.end( coordinate), num.mark and seg mean. I would like to > create the same file ( with 6 columns) but only containing information from > chromosome 1, then another one for 2 then 3...Y. Could somebody help please? > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] cghMCR_1.8.0 limma_3.4.3 CNTools_1.6.0 genefilter_1.32.0 > [5] DNAcopy_1.24.0 > > loaded via a namespace (and not attached): > [1] annotate_1.26.0 AnnotationDbi_1.10.1 Biobase_2.8.0 > [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.11.1 > [7] survival_2.35-8 xtable_1.5-6 > > thanks a lot > Nathalie > > > ID chrom loc.start loc.end num.mark seg.mean > 1 X10Th.txt 1 3002738 4.2E+07 3202 > -0.0163 > 2 X10Th.txt 1 4.2E+07 4.2E+07 2 > -0.7027 > 3 X10Th.txt 1 4.2E+07 1.7E+08 10731 > 0.0081 > 4 X10Th.txt 1 1.7E+08 1.7E+08 11 > 0.7461 > 5 X10Th.txt 1 1.7E+08 2.0E+08 2448 > -0.0052 > 6 X10Th.txt 10 3002742 1.3E+08 11833 > -0.0574 > 7 X10Th.txt 11 3026911 3100146 12 > -0.4499 > 8 X10Th.txt 11 3102021 3.4E+07 2516 > 0.007 > 9 X10Th.txt 11 3.4E+07 3.4E+07 4 > 0.7885 > 10 X10Th.txt 11 3.4E+07 7.1E+07 3834 > -0.0119 > 11 X10Th.txt 11 7.1E+07 7.1E+07 10 > -1.5455 > 12 X10Th.txt 11 7.1E+07 8.3E+07 1618 > 0.0099 > 13 X10Th.txt 11 8.3E+07 8.4E+07 2 > -1.9797 > 14 X10Th.txt 11 8.4E+07 9.0E+07 739 > 0.0197 > 15 X10Th.txt 11 9.0E+07 9.0E+07 3 > 0.4815 > 16 X10Th.txt 11 9.0E+07 1.2E+08 3920 > -0.0171 > 17 X10Th.txt 12 3095298 6.3E+07 4424 > 0.0474 > 18 X10Th.txt 12 6.3E+07 6.3E+07 3 > 0.5165 > 19 X10Th.txt 12 6.3E+07 1.1E+08 5209 > 0.0385 > 20 X10Th.txt 12 1.1E+08 1.1E+08 6 > -0.4526 > 21 X10Th.txt 12 1.1E+08 1.2E+08 201 > 0.1305 > 22 X10Th.txt 12 1.2E+08 1.2E+08 19 > 0.614 > 23 X10Th.txt 12 1.2E+08 1.2E+08 481 > 0.0334 > 24 X10Th.txt 13 3004789 1.2E+08 10642 > -0.3045 > 25 X10Th.txt 14 3892581 5.2E+07 4281 > 0.5563 > 26 X10Th.txt 14 5.2E+07 5.2E+07 4 > -0.4408 > 27 X10Th.txt 14 5.2E+07 5.2E+07 11 > -1.4074 > 28 X10Th.txt 14 5.2E+07 5.3E+07 12 > -0.6649 > 29 X10Th.txt 14 5.3E+07 5.3E+07 18 > -1.5591 > 30 X10Th.txt 14 5.3E+07 5.3E+07 56 > -2.6024 > 31 X10Th.txt 14 5.3E+07 6.8E+07 1815 > 0.5608 > 32 X10Th.txt 14 6.8E+07 6.8E+07 33 > 0.1478 > 33 X10Th.txt 14 6.8E+07 1.2E+08 4457 > 0.5724 > 34 X10Th.txt 15 3091692 3.9E+07 2821 > 0.6079 > 35 X10Th.txt 15 3.9E+07 3.9E+07 5 > 0.1051 > 36 X10Th.txt 15 3.9E+07 3.9E+07 12 > 0.5436 > 37 X10Th.txt 15 3.9E+07 3.9E+07 2 > -0.8667 > 38 X10Th.txt 15 3.9E+07 1.0E+08 6464 > 0.6688 > 39 X10Th.txt 16 3151162 6024268 339 > -0.1676 > 40 X10Th.txt 16 6032525 6045766 3 > -2.3133 > 41 X10Th.txt 16 6056091 3.6E+07 3366 > -0.136 > 42 X10Th.txt 16 3.6E+07 3.6E+07 4 > -1.392 > 43 X10Th.txt 16 3.6E+07 9.8E+07 5329 > -0.1383 > 44 X10Th.txt 17 3009074 9.5E+07 9007 > -0.1542 > 45 X10Th.txt 18 3181133 9.1E+07 8058 > -0.0622 > 46 X10Th.txt 19 3147156 1.7E+07 1848 > -0.3487 > 47 X10Th.txt 19 1.7E+07 1.8E+07 100 > -0.9124 > 48 X10Th.txt 19 1.8E+07 6.1E+07 4443 > -0.3708 > 49 X10Th.txt 2 3010301 3.1E+07 2777 > 0.1381 > 50 X10Th.txt 2 3.1E+07 3.1E+07 4 > -0.3156 > 51 X10Th.txt 2 3.1E+07 7.2E+07 3546 > 0.1484 > 52 X10Th.txt 2 7.2E+07 7.2E+07 2 > -0.4492 > 53 X10Th.txt 2 7.2E+07 9.0E+07 1994 > 0.1389 > 54 X10Th.txt 2 9.0E+07 9.0E+07 2 > 0.7181 > 55 X10Th.txt 2 9.0E+07 9.1E+07 192 > 0.1815 > 56 X10Th.txt 2 9.1E+07 9.1E+07 4 > 0.6128 > 57 X10Th.txt 2 9.1E+07 1.8E+08 8335 > 0.1312 > 58 X10Th.txt 3 3007185 1.4E+08 11302 > -0.1118 > 59 X10Th.txt 3 1.4E+08 1.4E+08 3 > 1.1729 > 60 X10Th.txt 3 1.4E+08 1.6E+08 1828 > -0.1205 > 61 X10Th.txt 4 3012291 3335299 10 > 0.0708 > 62 X10Th.txt 4 3353037 9459467 498 > 0.6502 > 63 X10Th.txt 4 9469402 9469402 3 > -0.1167 > 64 X10Th.txt 4 9473906 1.1E+07 123 > 0.8942 > 65 X10Th.txt 4 1.1E+07 1.4E+07 253 > 0.334 > 66 X10Th.txt 4 1.5E+07 1.6E+07 150 > 0.8265 > 67 X10Th.txt 4 1.6E+07 1.9E+07 179 > 0.322 > 68 X10Th.txt 4 1.9E+07 2.5E+07 463 > 0.8283 > 69 X10Th.txt 4 2.5E+07 2.5E+07 2 > -4.1559 > 70 X10Th.txt 4 2.5E+07 3.7E+07 759 > 0.8149 > 71 X10Th.txt 4 3.7E+07 3.7E+07 20 > 1.2765 > 72 X10Th.txt 4 3.7E+07 5.9E+07 1833 > 0.4829 > 73 X10Th.txt 4 5.9E+07 6E+07 83 1.0287 > 74 X10Th.txt 4 6.0E+07 6.6E+07 455 > 0.623 > 75 X10Th.txt 4 6.6E+07 6.6E+07 3 > -4.8121 > 76 X10Th.txt 4 6.6E+07 8.7E+07 1509 > 0.4519 > 77 X10Th.txt 4 8.7E+07 8.8E+07 37 > 0.9291 > 78 X10Th.txt 4 8.8E+07 9.7E+07 764 > 0.3171 > 79 X10Th.txt 4 9.7E+07 1.0E+08 417 > 0.8177 > 80 X10Th.txt 4 1.0E+08 1.0E+08 35 > 1.3066 > 81 X10Th.txt 4 1.0E+08 1.1E+08 1125 > 0.7607 > 82 X10Th.txt 4 1.1E+08 1.2E+08 933 > 0.3508 > 83 X10Th.txt 4 1.2E+08 1.2E+08 192 > 0.8091 > 84 X10Th.txt 4 1.2E+08 1.2E+08 15 > 1.3286 > 85 X10Th.txt 4 1.2E+08 1.2E+08 78 > 0.8328 > 86 X10Th.txt 4 1.2E+08 1.4E+08 1514 > 0.3228 > 87 X10Th.txt 4 1.4E+08 1.4E+08 3 > 1.2655 > 88 X10Th.txt 4 1.4E+08 1.5E+08 1352 > 0.283 > 89 X10Th.txt 4 1.5E+08 1.5E+08 41 > 0.8091 > 90 X10Th.txt 4 1.5E+08 1.6E+08 793 > 0.2844 > 91 X10Th.txt 5 3003879 3.3E+07 2707 > 0.105 > 92 X10Th.txt 5 3.3E+07 3.3E+07 3 > -0.6753 > 93 X10Th.txt 5 3.3E+07 9.4E+07 5039 > 0.1072 > 94 X10Th.txt 5 9.4E+07 9.6E+07 8 > -0.8031 > 95 X10Th.txt 5 9.6E+07 1.5E+08 6236 > 0.1028 > 96 X10Th.txt 6 3024849 2.6E+07 1843 > -0.1733 > 97 X10Th.txt 6 2.6E+07 2.6E+07 2 > -0.773 > 98 X10Th.txt 6 2.6E+07 3.4E+07 864 > -0.1393 > 99 X10Th.txt 6 3.4E+07 3.4E+07 3 > -2.5977 > 100 X10Th.txt 6 3.4E+07 4.1E+07 744 > -0.1363 > 101 X10Th.txt 6 4.1E+07 4.1E+07 60 > -0.9053 > 102 X10Th.txt 6 4.1E+07 1.2E+08 7693 > -0.1561 > 103 X10Th.txt 6 1.2E+08 1.2E+08 2 > 0.5483 > 104 X10Th.txt 6 1.2E+08 1.5E+08 2924 > -0.1333 > 105 X10Th.txt 7 3049177 2.9E+07 2215 > -0.174 > 106 X10Th.txt 7 2.9E+07 2.9E+07 3 > -0.8632 > 107 X10Th.txt 7 2.9E+07 3.4E+07 496 > -0.1613 > 108 X10Th.txt 7 3.4E+07 3.5E+07 55 > -0.6911 > 109 X10Th.txt 7 3.5E+07 1.0E+08 6236 > -0.1745 > 110 X10Th.txt 7 1.0E+08 1.0E+08 5 > -1.4229 > 111 X10Th.txt 7 1.0E+08 1.0E+08 20 > -0.1964 > 112 X10Th.txt 7 1.0E+08 1.0E+08 6 > -1.8286 > 113 X10Th.txt 7 1.0E+08 1.5E+08 4582 > -0.1627 > 114 X10Th.txt 8 3111085 1.3E+08 11524 > -0.1437 > 115 X10Th.txt 9 3088282 1.2E+08 12045 > 0.2501 > 116 X10Th.txt X 3086068 1.7E+08 12085 > -0.0107 > 117 X10Th.txt Y 27 263780 52 -1.2383 > 118 X10Th.txt Y 263932 631098 15 -0.5181 > 119 X10Th.txt Y 631698 2177516 532 -1.256 > 120 X11Th.txt 1 3002738 2.0E+08 16394 > -0.046 > 121 X11Th.txt 10 3002742 2.2E+07 1710 > -0.2582 > 122 X11Th.txt 10 2.2E+07 2.2E+07 2 > -2.3611 > 123 X11Th.txt 10 2.2E+07 1.3E+08 10121 > -0.2586 > 124 X11Th.txt 11 3026911 3.4E+07 2528 > -0.049 > 125 X11Th.txt 11 3.4E+07 3.4E+07 5 > 1.0058 > 126 X11Th.txt 11 3.4E+07 1.2E+08 10125 > -0.035 > 127 X11Th.txt 12 3095298 6.3E+07 4424 > -0.0904 > 128 X11Th.txt 12 6.3E+07 6.3E+07 3 > 1.7028 > 129 X11Th.txt 12 6.3E+07 1.2E+08 5916 > -0.0654 > 130 X11Th.txt 13 3004789 1.3E+07 854 > -0.1304 > 131 X11Th.txt 13 1.3E+07 1.3E+07 5 > -1.3861 > 132 X11Th.txt 13 1.3E+07 2.8E+07 1591 > -0.1782 > 133 X11Th.txt 13 2.8E+07 2.8E+07 5 > -1.3185 > 134 X11Th.txt 13 2.8E+07 6.5E+07 3634 > -0.1527 > 135 X11Th.txt 13 6.6E+07 6.7E+07 8 > -1.1874 > 136 X11Th.txt 13 6.7E+07 6.9E+07 201 > -0.1626 > 137 X11Th.txt 13 6.9E+07 6.9E+07 4 > 1.0844 > 138 X11Th.txt 13 6.9E+07 1.2E+08 4340 > -0.1625 > 139 X11Th.txt 14 3892581 5.3E+07 4319 > 0.6606 > 140 X11Th.txt 14 5.3E+07 5.3E+07 58 > -1.4906 > 141 X11Th.txt 14 5.3E+07 1.2E+08 6310 > 0.6554 > 142 X11Th.txt 15 3091692 8039326 448 > 0.4734 > 143 X11Th.txt 15 8040778 8040778 3 > 1.6185 > 144 X11Th.txt 15 8046698 3.9E+07 2358 > 0.454 > 145 X11Th.txt 15 3.9E+07 3.9E+07 3 > 1.5325 > 146 X11Th.txt 15 3.9E+07 1.0E+08 6492 > 0.4605 > 147 X11Th.txt 16 3151162 9.8E+07 9041 > -0.2314 > 148 X11Th.txt 17 3009074 9.5E+07 9007 > -0.0573 > 149 X11Th.txt 18 3181133 9.1E+07 8058 > 0.0341 > 150 X11Th.txt 19 3147156 6.1E+07 6391 > -0.1194 > 151 X11Th.txt 2 3010301 5.0E+07 4560 > 0.1442 > 152 X11Th.txt 2 5.0E+07 5.0E+07 4 > 1.1306 > 153 X11Th.txt 2 5.0E+07 1.8E+08 12292 > 0.1487 > 154 X11Th.txt 3 3007185 6032558 245 > -0.2823 > 155 X11Th.txt 3 6056822 6072724 3 > 1.2882 > 156 X11Th.txt 3 6083291 1.6E+08 12885 > -0.2812 > 157 X11Th.txt 4 3012291 3146483 5 > -0.8101 > 158 X11Th.txt 4 3159538 1.6E+08 13637 > 0.2846 > 159 X11Th.txt 5 3003879 1.1E+07 656 > 0.0416 > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, > a charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered office is 215 Euston Road, > London, NW1 2BE. > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Brian Herb Graduate Program in Biochemistry, Cellular and Molecular Biology Johns Hopkins School of Medicine Dr. Andrew Feinberg Laboratory Rangos 580 855 N. Wolfe St. Baltimore, MD 21205 Phone:410-614-3478 Fax: 410-614-9819 [[alternative HTML version deleted]]
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Since we're playing code golf, just wanted to point out: On Thu, Jul 14, 2011 at 10:44 AM, Brian Herb <brianherb at="" jhmi.edu=""> wrote: > Nathalie- > > try- > > chr1=subset(object,object$chrom==1) > > where object is your dataframe The cool thing about subset is that the column names of the data.frame you are working with are "injected" into the scope of the expression you are using a logical subset, so instead of: chr1 <- subset(object, object$chrom == 1) You can do chr1 <- subset(object, chrom == 1) Ain't that something? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 10.3 years ago
If X is your data.frame, try X.chrom <- split(X, X$chrom) This will create a list, with a dataframe for eah unique entry in the "chrom" column. HTH \Heidi > HI , > I want to subset a list I have in order to look only the data from > chosen chromosomes. > my file is this format ( see attached for a workable example) . This > dataframe contain 6 columns, ID (X10th.txt., X11th.txt..), > chrom(1---X,Y), loc.start and loc.end( coordinate), num.mark and seg > mean. I would like to create the same file ( with 6 columns) but only > containing information from chromosome 1, then another one for 2 then > 3...Y. Could somebody help please? > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] cghMCR_1.8.0 limma_3.4.3 CNTools_1.6.0 genefilter_1.32.0 > [5] DNAcopy_1.24.0 > > loaded via a namespace (and not attached): > [1] annotate_1.26.0 AnnotationDbi_1.10.1 Biobase_2.8.0 > [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.11.1 > [7] survival_2.35-8 xtable_1.5-6 > > thanks a lot > Nathalie > > > ID chrom loc.start loc.end num.mark seg.mean > 1 X10Th.txt 1 3002738 4.2E+07 3202 -0.0163 > 2 X10Th.txt 1 4.2E+07 4.2E+07 2 -0.7027 > 3 X10Th.txt 1 4.2E+07 1.7E+08 10731 0.0081 > 4 X10Th.txt 1 1.7E+08 1.7E+08 11 0.7461 > 5 X10Th.txt 1 1.7E+08 2.0E+08 2448 -0.0052 > 6 X10Th.txt 10 3002742 1.3E+08 11833 -0.0574 > 7 X10Th.txt 11 3026911 3100146 12 -0.4499 > 8 X10Th.txt 11 3102021 3.4E+07 2516 0.007 > 9 X10Th.txt 11 3.4E+07 3.4E+07 4 0.7885 > 10 X10Th.txt 11 3.4E+07 7.1E+07 3834 -0.0119 > 11 X10Th.txt 11 7.1E+07 7.1E+07 10 -1.5455 > 12 X10Th.txt 11 7.1E+07 8.3E+07 1618 0.0099 > 13 X10Th.txt 11 8.3E+07 8.4E+07 2 -1.9797 > 14 X10Th.txt 11 8.4E+07 9.0E+07 739 0.0197 > 15 X10Th.txt 11 9.0E+07 9.0E+07 3 0.4815 > 16 X10Th.txt 11 9.0E+07 1.2E+08 3920 -0.0171 > 17 X10Th.txt 12 3095298 6.3E+07 4424 0.0474 > 18 X10Th.txt 12 6.3E+07 6.3E+07 3 0.5165 > 19 X10Th.txt 12 6.3E+07 1.1E+08 5209 0.0385 > 20 X10Th.txt 12 1.1E+08 1.1E+08 6 -0.4526 > 21 X10Th.txt 12 1.1E+08 1.2E+08 201 0.1305 > 22 X10Th.txt 12 1.2E+08 1.2E+08 19 0.614 > 23 X10Th.txt 12 1.2E+08 1.2E+08 481 0.0334 > 24 X10Th.txt 13 3004789 1.2E+08 10642 -0.3045 > 25 X10Th.txt 14 3892581 5.2E+07 4281 0.5563 > 26 X10Th.txt 14 5.2E+07 5.2E+07 4 -0.4408 > 27 X10Th.txt 14 5.2E+07 5.2E+07 11 -1.4074 > 28 X10Th.txt 14 5.2E+07 5.3E+07 12 -0.6649 > 29 X10Th.txt 14 5.3E+07 5.3E+07 18 -1.5591 > 30 X10Th.txt 14 5.3E+07 5.3E+07 56 -2.6024 > 31 X10Th.txt 14 5.3E+07 6.8E+07 1815 0.5608 > 32 X10Th.txt 14 6.8E+07 6.8E+07 33 0.1478 > 33 X10Th.txt 14 6.8E+07 1.2E+08 4457 0.5724 > 34 X10Th.txt 15 3091692 3.9E+07 2821 0.6079 > 35 X10Th.txt 15 3.9E+07 3.9E+07 5 0.1051 > 36 X10Th.txt 15 3.9E+07 3.9E+07 12 0.5436 > 37 X10Th.txt 15 3.9E+07 3.9E+07 2 -0.8667 > 38 X10Th.txt 15 3.9E+07 1.0E+08 6464 0.6688 > 39 X10Th.txt 16 3151162 6024268 339 -0.1676 > 40 X10Th.txt 16 6032525 6045766 3 -2.3133 > 41 X10Th.txt 16 6056091 3.6E+07 3366 -0.136 > 42 X10Th.txt 16 3.6E+07 3.6E+07 4 -1.392 > 43 X10Th.txt 16 3.6E+07 9.8E+07 5329 -0.1383 > 44 X10Th.txt 17 3009074 9.5E+07 9007 -0.1542 > 45 X10Th.txt 18 3181133 9.1E+07 8058 -0.0622 > 46 X10Th.txt 19 3147156 1.7E+07 1848 -0.3487 > 47 X10Th.txt 19 1.7E+07 1.8E+07 100 -0.9124 > 48 X10Th.txt 19 1.8E+07 6.1E+07 4443 -0.3708 > 49 X10Th.txt 2 3010301 3.1E+07 2777 0.1381 > 50 X10Th.txt 2 3.1E+07 3.1E+07 4 -0.3156 > 51 X10Th.txt 2 3.1E+07 7.2E+07 3546 0.1484 > 52 X10Th.txt 2 7.2E+07 7.2E+07 2 -0.4492 > 53 X10Th.txt 2 7.2E+07 9.0E+07 1994 0.1389 > 54 X10Th.txt 2 9.0E+07 9.0E+07 2 0.7181 > 55 X10Th.txt 2 9.0E+07 9.1E+07 192 0.1815 > 56 X10Th.txt 2 9.1E+07 9.1E+07 4 0.6128 > 57 X10Th.txt 2 9.1E+07 1.8E+08 8335 0.1312 > 58 X10Th.txt 3 3007185 1.4E+08 11302 -0.1118 > 59 X10Th.txt 3 1.4E+08 1.4E+08 3 1.1729 > 60 X10Th.txt 3 1.4E+08 1.6E+08 1828 -0.1205 > 61 X10Th.txt 4 3012291 3335299 10 0.0708 > 62 X10Th.txt 4 3353037 9459467 498 0.6502 > 63 X10Th.txt 4 9469402 9469402 3 -0.1167 > 64 X10Th.txt 4 9473906 1.1E+07 123 0.8942 > 65 X10Th.txt 4 1.1E+07 1.4E+07 253 0.334 > 66 X10Th.txt 4 1.5E+07 1.6E+07 150 0.8265 > 67 X10Th.txt 4 1.6E+07 1.9E+07 179 0.322 > 68 X10Th.txt 4 1.9E+07 2.5E+07 463 0.8283 > 69 X10Th.txt 4 2.5E+07 2.5E+07 2 -4.1559 > 70 X10Th.txt 4 2.5E+07 3.7E+07 759 0.8149 > 71 X10Th.txt 4 3.7E+07 3.7E+07 20 1.2765 > 72 X10Th.txt 4 3.7E+07 5.9E+07 1833 0.4829 > 73 X10Th.txt 4 5.9E+07 6E+07 83 1.0287 > 74 X10Th.txt 4 6.0E+07 6.6E+07 455 0.623 > 75 X10Th.txt 4 6.6E+07 6.6E+07 3 -4.8121 > 76 X10Th.txt 4 6.6E+07 8.7E+07 1509 0.4519 > 77 X10Th.txt 4 8.7E+07 8.8E+07 37 0.9291 > 78 X10Th.txt 4 8.8E+07 9.7E+07 764 0.3171 > 79 X10Th.txt 4 9.7E+07 1.0E+08 417 0.8177 > 80 X10Th.txt 4 1.0E+08 1.0E+08 35 1.3066 > 81 X10Th.txt 4 1.0E+08 1.1E+08 1125 0.7607 > 82 X10Th.txt 4 1.1E+08 1.2E+08 933 0.3508 > 83 X10Th.txt 4 1.2E+08 1.2E+08 192 0.8091 > 84 X10Th.txt 4 1.2E+08 1.2E+08 15 1.3286 > 85 X10Th.txt 4 1.2E+08 1.2E+08 78 0.8328 > 86 X10Th.txt 4 1.2E+08 1.4E+08 1514 0.3228 > 87 X10Th.txt 4 1.4E+08 1.4E+08 3 1.2655 > 88 X10Th.txt 4 1.4E+08 1.5E+08 1352 0.283 > 89 X10Th.txt 4 1.5E+08 1.5E+08 41 0.8091 > 90 X10Th.txt 4 1.5E+08 1.6E+08 793 0.2844 > 91 X10Th.txt 5 3003879 3.3E+07 2707 0.105 > 92 X10Th.txt 5 3.3E+07 3.3E+07 3 -0.6753 > 93 X10Th.txt 5 3.3E+07 9.4E+07 5039 0.1072 > 94 X10Th.txt 5 9.4E+07 9.6E+07 8 -0.8031 > 95 X10Th.txt 5 9.6E+07 1.5E+08 6236 0.1028 > 96 X10Th.txt 6 3024849 2.6E+07 1843 -0.1733 > 97 X10Th.txt 6 2.6E+07 2.6E+07 2 -0.773 > 98 X10Th.txt 6 2.6E+07 3.4E+07 864 -0.1393 > 99 X10Th.txt 6 3.4E+07 3.4E+07 3 -2.5977 > 100 X10Th.txt 6 3.4E+07 4.1E+07 744 -0.1363 > 101 X10Th.txt 6 4.1E+07 4.1E+07 60 -0.9053 > 102 X10Th.txt 6 4.1E+07 1.2E+08 7693 -0.1561 > 103 X10Th.txt 6 1.2E+08 1.2E+08 2 0.5483 > 104 X10Th.txt 6 1.2E+08 1.5E+08 2924 -0.1333 > 105 X10Th.txt 7 3049177 2.9E+07 2215 -0.174 > 106 X10Th.txt 7 2.9E+07 2.9E+07 3 -0.8632 > 107 X10Th.txt 7 2.9E+07 3.4E+07 496 -0.1613 > 108 X10Th.txt 7 3.4E+07 3.5E+07 55 -0.6911 > 109 X10Th.txt 7 3.5E+07 1.0E+08 6236 -0.1745 > 110 X10Th.txt 7 1.0E+08 1.0E+08 5 -1.4229 > 111 X10Th.txt 7 1.0E+08 1.0E+08 20 -0.1964 > 112 X10Th.txt 7 1.0E+08 1.0E+08 6 -1.8286 > 113 X10Th.txt 7 1.0E+08 1.5E+08 4582 -0.1627 > 114 X10Th.txt 8 3111085 1.3E+08 11524 -0.1437 > 115 X10Th.txt 9 3088282 1.2E+08 12045 0.2501 > 116 X10Th.txt X 3086068 1.7E+08 12085 -0.0107 > 117 X10Th.txt Y 27 263780 52 -1.2383 > 118 X10Th.txt Y 263932 631098 15 -0.5181 > 119 X10Th.txt Y 631698 2177516 532 -1.256 > 120 X11Th.txt 1 3002738 2.0E+08 16394 -0.046 > 121 X11Th.txt 10 3002742 2.2E+07 1710 -0.2582 > 122 X11Th.txt 10 2.2E+07 2.2E+07 2 -2.3611 > 123 X11Th.txt 10 2.2E+07 1.3E+08 10121 -0.2586 > 124 X11Th.txt 11 3026911 3.4E+07 2528 -0.049 > 125 X11Th.txt 11 3.4E+07 3.4E+07 5 1.0058 > 126 X11Th.txt 11 3.4E+07 1.2E+08 10125 -0.035 > 127 X11Th.txt 12 3095298 6.3E+07 4424 -0.0904 > 128 X11Th.txt 12 6.3E+07 6.3E+07 3 1.7028 > 129 X11Th.txt 12 6.3E+07 1.2E+08 5916 -0.0654 > 130 X11Th.txt 13 3004789 1.3E+07 854 -0.1304 > 131 X11Th.txt 13 1.3E+07 1.3E+07 5 -1.3861 > 132 X11Th.txt 13 1.3E+07 2.8E+07 1591 -0.1782 > 133 X11Th.txt 13 2.8E+07 2.8E+07 5 -1.3185 > 134 X11Th.txt 13 2.8E+07 6.5E+07 3634 -0.1527 > 135 X11Th.txt 13 6.6E+07 6.7E+07 8 -1.1874 > 136 X11Th.txt 13 6.7E+07 6.9E+07 201 -0.1626 > 137 X11Th.txt 13 6.9E+07 6.9E+07 4 1.0844 > 138 X11Th.txt 13 6.9E+07 1.2E+08 4340 -0.1625 > 139 X11Th.txt 14 3892581 5.3E+07 4319 0.6606 > 140 X11Th.txt 14 5.3E+07 5.3E+07 58 -1.4906 > 141 X11Th.txt 14 5.3E+07 1.2E+08 6310 0.6554 > 142 X11Th.txt 15 3091692 8039326 448 0.4734 > 143 X11Th.txt 15 8040778 8040778 3 1.6185 > 144 X11Th.txt 15 8046698 3.9E+07 2358 0.454 > 145 X11Th.txt 15 3.9E+07 3.9E+07 3 1.5325 > 146 X11Th.txt 15 3.9E+07 1.0E+08 6492 0.4605 > 147 X11Th.txt 16 3151162 9.8E+07 9041 -0.2314 > 148 X11Th.txt 17 3009074 9.5E+07 9007 -0.0573 > 149 X11Th.txt 18 3181133 9.1E+07 8058 0.0341 > 150 X11Th.txt 19 3147156 6.1E+07 6391 -0.1194 > 151 X11Th.txt 2 3010301 5.0E+07 4560 0.1442 > 152 X11Th.txt 2 5.0E+07 5.0E+07 4 1.1306 > 153 X11Th.txt 2 5.0E+07 1.8E+08 12292 0.1487 > 154 X11Th.txt 3 3007185 6032558 245 -0.2823 > 155 X11Th.txt 3 6056822 6072724 3 1.2882 > 156 X11Th.txt 3 6083291 1.6E+08 12885 -0.2812 > 157 X11Th.txt 4 3012291 3146483 5 -0.8101 > 158 X11Th.txt 4 3159538 1.6E+08 13637 0.2846 > 159 X11Th.txt 5 3003879 1.1E+07 656 0.0416 > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Ramzi TEMANNI ▴ 160
@ramzi-temanni-3819
Last seen 10.3 years ago
Hi Nathalie, this code sould give you the expected results: data=read.table("data.csv",header=T) # read data file for (i in unique(data$chrom) ) { write.table(data[which(data$chrom==i),],paste("data",i,".csv",sep=""), row.names=F) # generate 1 file per Chr } Best, Ramzi TEMANNI http://www.linkedin.com/in/ramzitemanni On Thu, Jul 14, 2011 at 4:34 PM, Nathalie Conte <nac@sanger.ac.uk> wrote: > HI , > I want to subset a list I have in order to look only the data from chosen > chromosomes. > my file is this format ( see attached for a workable example) . This > dataframe contain 6 columns, ID (X10th.txt., X11th.txt..), chrom(1 ---X,Y), > loc.start and loc.end( coordinate), num.mark and seg mean. I would like to > create the same file ( with 6 columns) but only containing information from > chromosome 1, then another one for 2 then 3...Y. Could somebody help please? > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] cghMCR_1.8.0 limma_3.4.3 CNTools_1.6.0 genefilter_1.32.0 > [5] DNAcopy_1.24.0 > > loaded via a namespace (and not attached): > [1] annotate_1.26.0 AnnotationDbi_1.10.1 Biobase_2.8.0 > [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.11.1 > [7] survival_2.35-8 xtable_1.5-6 > > thanks a lot > Nathalie > > > ID chrom loc.start loc.end num.mark seg.mean > 1 X10Th.txt 1 3002738 4.2E+07 3202 > -0.0163 > 2 X10Th.txt 1 4.2E+07 4.2E+07 2 > -0.7027 > 3 X10Th.txt 1 4.2E+07 1.7E+08 10731 > 0.0081 > 4 X10Th.txt 1 1.7E+08 1.7E+08 11 > 0.7461 > 5 X10Th.txt 1 1.7E+08 2.0E+08 2448 > -0.0052 > 6 X10Th.txt 10 3002742 1.3E+08 11833 > -0.0574 > 7 X10Th.txt 11 3026911 3100146 12 > -0.4499 > 8 X10Th.txt 11 3102021 3.4E+07 2516 > 0.007 > 9 X10Th.txt 11 3.4E+07 3.4E+07 4 > 0.7885 > 10 X10Th.txt 11 3.4E+07 7.1E+07 3834 > -0.0119 > 11 X10Th.txt 11 7.1E+07 7.1E+07 10 > -1.5455 > 12 X10Th.txt 11 7.1E+07 8.3E+07 1618 > 0.0099 > 13 X10Th.txt 11 8.3E+07 8.4E+07 2 > -1.9797 > 14 X10Th.txt 11 8.4E+07 9.0E+07 739 > 0.0197 > 15 X10Th.txt 11 9.0E+07 9.0E+07 3 > 0.4815 > 16 X10Th.txt 11 9.0E+07 1.2E+08 3920 > -0.0171 > 17 X10Th.txt 12 3095298 6.3E+07 4424 > 0.0474 > 18 X10Th.txt 12 6.3E+07 6.3E+07 3 > 0.5165 > 19 X10Th.txt 12 6.3E+07 1.1E+08 5209 > 0.0385 > 20 X10Th.txt 12 1.1E+08 1.1E+08 6 > -0.4526 > 21 X10Th.txt 12 1.1E+08 1.2E+08 201 > 0.1305 > 22 X10Th.txt 12 1.2E+08 1.2E+08 19 > 0.614 > 23 X10Th.txt 12 1.2E+08 1.2E+08 481 > 0.0334 > 24 X10Th.txt 13 3004789 1.2E+08 10642 > -0.3045 > 25 X10Th.txt 14 3892581 5.2E+07 4281 > 0.5563 > 26 X10Th.txt 14 5.2E+07 5.2E+07 4 > -0.4408 > 27 X10Th.txt 14 5.2E+07 5.2E+07 11 > -1.4074 > 28 X10Th.txt 14 5.2E+07 5.3E+07 12 > -0.6649 > 29 X10Th.txt 14 5.3E+07 5.3E+07 18 > -1.5591 > 30 X10Th.txt 14 5.3E+07 5.3E+07 56 > -2.6024 > 31 X10Th.txt 14 5.3E+07 6.8E+07 1815 > 0.5608 > 32 X10Th.txt 14 6.8E+07 6.8E+07 33 > 0.1478 > 33 X10Th.txt 14 6.8E+07 1.2E+08 4457 > 0.5724 > 34 X10Th.txt 15 3091692 3.9E+07 2821 > 0.6079 > 35 X10Th.txt 15 3.9E+07 3.9E+07 5 > 0.1051 > 36 X10Th.txt 15 3.9E+07 3.9E+07 12 > 0.5436 > 37 X10Th.txt 15 3.9E+07 3.9E+07 2 > -0.8667 > 38 X10Th.txt 15 3.9E+07 1.0E+08 6464 > 0.6688 > 39 X10Th.txt 16 3151162 6024268 339 > -0.1676 > 40 X10Th.txt 16 6032525 6045766 3 > -2.3133 > 41 X10Th.txt 16 6056091 3.6E+07 3366 > -0.136 > 42 X10Th.txt 16 3.6E+07 3.6E+07 4 > -1.392 > 43 X10Th.txt 16 3.6E+07 9.8E+07 5329 > -0.1383 > 44 X10Th.txt 17 3009074 9.5E+07 9007 > -0.1542 > 45 X10Th.txt 18 3181133 9.1E+07 8058 > -0.0622 > 46 X10Th.txt 19 3147156 1.7E+07 1848 > -0.3487 > 47 X10Th.txt 19 1.7E+07 1.8E+07 100 > -0.9124 > 48 X10Th.txt 19 1.8E+07 6.1E+07 4443 > -0.3708 > 49 X10Th.txt 2 3010301 3.1E+07 2777 > 0.1381 > 50 X10Th.txt 2 3.1E+07 3.1E+07 4 > -0.3156 > 51 X10Th.txt 2 3.1E+07 7.2E+07 3546 > 0.1484 > 52 X10Th.txt 2 7.2E+07 7.2E+07 2 > -0.4492 > 53 X10Th.txt 2 7.2E+07 9.0E+07 1994 > 0.1389 > 54 X10Th.txt 2 9.0E+07 9.0E+07 2 > 0.7181 > 55 X10Th.txt 2 9.0E+07 9.1E+07 192 > 0.1815 > 56 X10Th.txt 2 9.1E+07 9.1E+07 4 > 0.6128 > 57 X10Th.txt 2 9.1E+07 1.8E+08 8335 > 0.1312 > 58 X10Th.txt 3 3007185 1.4E+08 11302 > -0.1118 > 59 X10Th.txt 3 1.4E+08 1.4E+08 3 > 1.1729 > 60 X10Th.txt 3 1.4E+08 1.6E+08 1828 > -0.1205 > 61 X10Th.txt 4 3012291 3335299 10 > 0.0708 > 62 X10Th.txt 4 3353037 9459467 498 > 0.6502 > 63 X10Th.txt 4 9469402 9469402 3 > -0.1167 > 64 X10Th.txt 4 9473906 1.1E+07 123 > 0.8942 > 65 X10Th.txt 4 1.1E+07 1.4E+07 253 > 0.334 > 66 X10Th.txt 4 1.5E+07 1.6E+07 150 > 0.8265 > 67 X10Th.txt 4 1.6E+07 1.9E+07 179 > 0.322 > 68 X10Th.txt 4 1.9E+07 2.5E+07 463 > 0.8283 > 69 X10Th.txt 4 2.5E+07 2.5E+07 2 > -4.1559 > 70 X10Th.txt 4 2.5E+07 3.7E+07 759 > 0.8149 > 71 X10Th.txt 4 3.7E+07 3.7E+07 20 > 1.2765 > 72 X10Th.txt 4 3.7E+07 5.9E+07 1833 > 0.4829 > 73 X10Th.txt 4 5.9E+07 6E+07 83 1.0287 > 74 X10Th.txt 4 6.0E+07 6.6E+07 455 > 0.623 > 75 X10Th.txt 4 6.6E+07 6.6E+07 3 > -4.8121 > 76 X10Th.txt 4 6.6E+07 8.7E+07 1509 > 0.4519 > 77 X10Th.txt 4 8.7E+07 8.8E+07 37 > 0.9291 > 78 X10Th.txt 4 8.8E+07 9.7E+07 764 > 0.3171 > 79 X10Th.txt 4 9.7E+07 1.0E+08 417 > 0.8177 > 80 X10Th.txt 4 1.0E+08 1.0E+08 35 > 1.3066 > 81 X10Th.txt 4 1.0E+08 1.1E+08 1125 > 0.7607 > 82 X10Th.txt 4 1.1E+08 1.2E+08 933 > 0.3508 > 83 X10Th.txt 4 1.2E+08 1.2E+08 192 > 0.8091 > 84 X10Th.txt 4 1.2E+08 1.2E+08 15 > 1.3286 > 85 X10Th.txt 4 1.2E+08 1.2E+08 78 > 0.8328 > 86 X10Th.txt 4 1.2E+08 1.4E+08 1514 > 0.3228 > 87 X10Th.txt 4 1.4E+08 1.4E+08 3 > 1.2655 > 88 X10Th.txt 4 1.4E+08 1.5E+08 1352 > 0.283 > 89 X10Th.txt 4 1.5E+08 1.5E+08 41 > 0.8091 > 90 X10Th.txt 4 1.5E+08 1.6E+08 793 > 0.2844 > 91 X10Th.txt 5 3003879 3.3E+07 2707 > 0.105 > 92 X10Th.txt 5 3.3E+07 3.3E+07 3 > -0.6753 > 93 X10Th.txt 5 3.3E+07 9.4E+07 5039 > 0.1072 > 94 X10Th.txt 5 9.4E+07 9.6E+07 8 > -0.8031 > 95 X10Th.txt 5 9.6E+07 1.5E+08 6236 > 0.1028 > 96 X10Th.txt 6 3024849 2.6E+07 1843 > -0.1733 > 97 X10Th.txt 6 2.6E+07 2.6E+07 2 > -0.773 > 98 X10Th.txt 6 2.6E+07 3.4E+07 864 > -0.1393 > 99 X10Th.txt 6 3.4E+07 3.4E+07 3 > -2.5977 > 100 X10Th.txt 6 3.4E+07 4.1E+07 744 > -0.1363 > 101 X10Th.txt 6 4.1E+07 4.1E+07 60 > -0.9053 > 102 X10Th.txt 6 4.1E+07 1.2E+08 7693 > -0.1561 > 103 X10Th.txt 6 1.2E+08 1.2E+08 2 > 0.5483 > 104 X10Th.txt 6 1.2E+08 1.5E+08 2924 > -0.1333 > 105 X10Th.txt 7 3049177 2.9E+07 2215 > -0.174 > 106 X10Th.txt 7 2.9E+07 2.9E+07 3 > -0.8632 > 107 X10Th.txt 7 2.9E+07 3.4E+07 496 > -0.1613 > 108 X10Th.txt 7 3.4E+07 3.5E+07 55 > -0.6911 > 109 X10Th.txt 7 3.5E+07 1.0E+08 6236 > -0.1745 > 110 X10Th.txt 7 1.0E+08 1.0E+08 5 > -1.4229 > 111 X10Th.txt 7 1.0E+08 1.0E+08 20 > -0.1964 > 112 X10Th.txt 7 1.0E+08 1.0E+08 6 > -1.8286 > 113 X10Th.txt 7 1.0E+08 1.5E+08 4582 > -0.1627 > 114 X10Th.txt 8 3111085 1.3E+08 11524 > -0.1437 > 115 X10Th.txt 9 3088282 1.2E+08 12045 > 0.2501 > 116 X10Th.txt X 3086068 1.7E+08 12085 > -0.0107 > 117 X10Th.txt Y 27 263780 52 -1.2383 > 118 X10Th.txt Y 263932 631098 15 -0.5181 > 119 X10Th.txt Y 631698 2177516 532 -1.256 > 120 X11Th.txt 1 3002738 2.0E+08 16394 > -0.046 > 121 X11Th.txt 10 3002742 2.2E+07 1710 > -0.2582 > 122 X11Th.txt 10 2.2E+07 2.2E+07 2 > -2.3611 > 123 X11Th.txt 10 2.2E+07 1.3E+08 10121 > -0.2586 > 124 X11Th.txt 11 3026911 3.4E+07 2528 > -0.049 > 125 X11Th.txt 11 3.4E+07 3.4E+07 5 > 1.0058 > 126 X11Th.txt 11 3.4E+07 1.2E+08 10125 > -0.035 > 127 X11Th.txt 12 3095298 6.3E+07 4424 > -0.0904 > 128 X11Th.txt 12 6.3E+07 6.3E+07 3 > 1.7028 > 129 X11Th.txt 12 6.3E+07 1.2E+08 5916 > -0.0654 > 130 X11Th.txt 13 3004789 1.3E+07 854 > -0.1304 > 131 X11Th.txt 13 1.3E+07 1.3E+07 5 > -1.3861 > 132 X11Th.txt 13 1.3E+07 2.8E+07 1591 > -0.1782 > 133 X11Th.txt 13 2.8E+07 2.8E+07 5 > -1.3185 > 134 X11Th.txt 13 2.8E+07 6.5E+07 3634 > -0.1527 > 135 X11Th.txt 13 6.6E+07 6.7E+07 8 > -1.1874 > 136 X11Th.txt 13 6.7E+07 6.9E+07 201 > -0.1626 > 137 X11Th.txt 13 6.9E+07 6.9E+07 4 > 1.0844 > 138 X11Th.txt 13 6.9E+07 1.2E+08 4340 > -0.1625 > 139 X11Th.txt 14 3892581 5.3E+07 4319 > 0.6606 > 140 X11Th.txt 14 5.3E+07 5.3E+07 58 > -1.4906 > 141 X11Th.txt 14 5.3E+07 1.2E+08 6310 > 0.6554 > 142 X11Th.txt 15 3091692 8039326 448 > 0.4734 > 143 X11Th.txt 15 8040778 8040778 3 > 1.6185 > 144 X11Th.txt 15 8046698 3.9E+07 2358 > 0.454 > 145 X11Th.txt 15 3.9E+07 3.9E+07 3 > 1.5325 > 146 X11Th.txt 15 3.9E+07 1.0E+08 6492 > 0.4605 > 147 X11Th.txt 16 3151162 9.8E+07 9041 > -0.2314 > 148 X11Th.txt 17 3009074 9.5E+07 9007 > -0.0573 > 149 X11Th.txt 18 3181133 9.1E+07 8058 > 0.0341 > 150 X11Th.txt 19 3147156 6.1E+07 6391 > -0.1194 > 151 X11Th.txt 2 3010301 5.0E+07 4560 > 0.1442 > 152 X11Th.txt 2 5.0E+07 5.0E+07 4 > 1.1306 > 153 X11Th.txt 2 5.0E+07 1.8E+08 12292 > 0.1487 > 154 X11Th.txt 3 3007185 6032558 245 > -0.2823 > 155 X11Th.txt 3 6056822 6072724 3 > 1.2882 > 156 X11Th.txt 3 6083291 1.6E+08 12885 > -0.2812 > 157 X11Th.txt 4 3012291 3146483 5 > -0.8101 > 158 X11Th.txt 4 3159538 1.6E+08 13637 > 0.2846 > 159 X11Th.txt 5 3003879 1.1E+07 656 > 0.0416 > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, > a charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered office is 215 Euston Road, > London, NW1 2BE. > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Ramzi TEMANNI ▴ 160
@ramzi-temanni-3819
Last seen 10.3 years ago
Best, Ramzi TEMANNI +31683862423 http://www.linkedin.com/in/ramzitemanni Hi Nathalie, sure you can easily do that by using the dir command: * files.list=dir(path = ".", pattern = "csv") * lest say you have files with extension csv the command dir will store the file names in myfiles then you loop over file.list and don't forget to change the paste part so you don't overwrite files. for (*myfile* in files.list) { data=read.table(...) .... for ... paste(*myfile*,"_",i,".**csv",sep="") ....} hope this answer your question. Best, Ramzi TEMANNI http://www.linkedin.com/in/**ramzitemanni<http: www.linkedin.com="" in="" r="" amzitemanni=""> On Thu, Jul 14, 2011 at 5:48 PM, Nathalie Conte <nac@sanger.ac.uk> wrote: > thanks Ramzi, the loop will save me a lot of time, is there a way to create > a loop to use read.table() of all tables in one go, for me to use them for > further analysis? > thanks again > Nat > >> Hi Nathalie, >> this code sould give you the expected results: >> data=read.table("data.csv",**header=T) # read data file >> for (i in unique(data$chrom) ) >> { >> write.table(data[which(data$**chrom==i),],paste("data",i,".**csv",s ep=""),row.names=F) >> # generate 1 file per Chr >> } >> >> >> >> >> >> Best, >> Ramzi TEMANNI >> http://www.linkedin.com/in/**ramzitemanni<http: www.linkedin.com="" i="" n="" ramzitemanni=""> >> >> >> >> On Thu, Jul 14, 2011 at 4:34 PM, Nathalie Conte <nac@sanger.ac.uk<mailto:>> nac@sanger.ac.uk>> wrote: >> >> HI , >> I want to subset a list I have in order to look only the data from >> chosen chromosomes. >> my file is this format ( see attached for a workable example) . >> This dataframe contain 6 columns, ID (X10th.txt., X11th.txt..), >> chrom(1---X,Y), loc.start and loc.end( coordinate), num.mark and >> seg mean. I would like to create the same file ( with 6 columns) >> but only containing information from chromosome 1, then another >> one for 2 then 3...Y. Could somebody help please? >> > sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=C >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] cghMCR_1.8.0 limma_3.4.3 CNTools_1.6.0 genefilter_1.32.0 >> [5] DNAcopy_1.24.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.26.0 AnnotationDbi_1.10.1 Biobase_2.8.0 >> [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.11.1 >> [7] survival_2.35-8 xtable_1.5-6 >> >> thanks a lot >> Nathalie >> >> >> ID chrom loc.start loc.end num.mark >> seg.mean >> 1 X10Th.txt 1 3002738 4.2E+07 3202 >> -0.0163 >> 2 X10Th.txt 1 4.2E+07 4.2E+07 2 >> -0.7027 >> 3 X10Th.txt 1 4.2E+07 1.7E+08 >> 10731 0.0081 >> 4 X10Th.txt 1 1.7E+08 1.7E+08 11 >> 0.7461 >> 5 X10Th.txt 1 1.7E+08 2.0E+08 2448 >> -0.0052 >> 6 X10Th.txt 10 3002742 1.3E+08 >> 11833 -0.0574 >> 7 X10Th.txt 11 3026911 3100146 >> <tel:3100146> 12 -0.4499 >> 8 X10Th.txt 11 3102021 <tel:3102021> >> 3.4E+07 2516 0.007 >> >> 9 X10Th.txt 11 3.4E+07 3.4E+07 4 >> 0.7885 >> 10 X10Th.txt 11 3.4E+07 7.1E+07 3834 >> -0.0119 >> 11 X10Th.txt 11 7.1E+07 7.1E+07 10 >> -1.5455 >> 12 X10Th.txt 11 7.1E+07 8.3E+07 1618 >> 0.0099 >> 13 X10Th.txt 11 8.3E+07 8.4E+07 2 >> -1.9797 >> 14 X10Th.txt 11 8.4E+07 9.0E+07 739 >> 0.0197 >> 15 X10Th.txt 11 9.0E+07 9.0E+07 3 >> 0.4815 >> 16 X10Th.txt 11 9.0E+07 1.2E+08 3920 >> -0.0171 >> 17 X10Th.txt 12 3095298 6.3E+07 4424 >> 0.0474 >> 18 X10Th.txt 12 6.3E+07 6.3E+07 3 >> 0.5165 >> 19 X10Th.txt 12 6.3E+07 1.1E+08 5209 >> 0.0385 >> 20 X10Th.txt 12 1.1E+08 1.1E+08 6 >> -0.4526 >> 21 X10Th.txt 12 1.1E+08 1.2E+08 201 >> 0.1305 >> 22 X10Th.txt 12 1.2E+08 1.2E+08 19 >> 0.614 >> 23 X10Th.txt 12 1.2E+08 1.2E+08 481 >> 0.0334 >> 24 X10Th.txt 13 3004789 1.2E+08 >> 10642 -0.3045 >> 25 X10Th.txt 14 3892581 5.2E+07 4281 >> 0.5563 >> 26 X10Th.txt 14 5.2E+07 5.2E+07 4 >> -0.4408 >> 27 X10Th.txt 14 5.2E+07 5.2E+07 11 >> -1.4074 >> 28 X10Th.txt 14 5.2E+07 5.3E+07 12 >> -0.6649 >> 29 X10Th.txt 14 5.3E+07 5.3E+07 18 >> -1.5591 >> 30 X10Th.txt 14 5.3E+07 5.3E+07 56 >> -2.6024 >> 31 X10Th.txt 14 5.3E+07 6.8E+07 1815 >> 0.5608 >> 32 X10Th.txt 14 6.8E+07 6.8E+07 33 >> 0.1478 >> 33 X10Th.txt 14 6.8E+07 1.2E+08 4457 >> 0.5724 >> 34 X10Th.txt 15 3091692 3.9E+07 2821 >> 0.6079 >> 35 X10Th.txt 15 3.9E+07 3.9E+07 5 >> 0.1051 >> 36 X10Th.txt 15 3.9E+07 3.9E+07 12 >> 0.5436 >> 37 X10Th.txt 15 3.9E+07 3.9E+07 2 >> -0.8667 >> 38 X10Th.txt 15 3.9E+07 1.0E+08 6464 >> 0.6688 >> 39 X10Th.txt 16 3151162 6024268 339 >> -0.1676 >> 40 X10Th.txt 16 6032525 6045766 3 >> -2.3133 >> 41 X10Th.txt 16 6056091 3.6E+07 3366 >> -0.136 >> 42 X10Th.txt 16 3.6E+07 3.6E+07 4 >> -1.392 >> 43 X10Th.txt 16 3.6E+07 9.8E+07 5329 >> -0.1383 >> 44 X10Th.txt 17 3009074 9.5E+07 9007 >> -0.1542 >> 45 X10Th.txt 18 3181133 9.1E+07 8058 >> -0.0622 >> 46 X10Th.txt 19 3147156 1.7E+07 1848 >> -0.3487 >> 47 X10Th.txt 19 1.7E+07 1.8E+07 100 >> -0.9124 >> 48 X10Th.txt 19 1.8E+07 6.1E+07 4443 >> -0.3708 >> 49 X10Th.txt 2 3010301 3.1E+07 2777 >> 0.1381 >> 50 X10Th.txt 2 3.1E+07 3.1E+07 4 >> -0.3156 >> 51 X10Th.txt 2 3.1E+07 7.2E+07 3546 >> 0.1484 >> 52 X10Th.txt 2 7.2E+07 7.2E+07 2 >> -0.4492 >> 53 X10Th.txt 2 7.2E+07 9.0E+07 1994 >> 0.1389 >> 54 X10Th.txt 2 9.0E+07 9.0E+07 2 >> 0.7181 >> 55 X10Th.txt 2 9.0E+07 9.1E+07 192 >> 0.1815 >> 56 X10Th.txt 2 9.1E+07 9.1E+07 4 >> 0.6128 >> 57 X10Th.txt 2 9.1E+07 1.8E+08 8335 >> 0.1312 >> 58 X10Th.txt 3 3007185 1.4E+08 >> 11302 -0.1118 >> 59 X10Th.txt 3 1.4E+08 1.4E+08 3 >> 1.1729 >> 60 X10Th.txt 3 1.4E+08 1.6E+08 1828 >> -0.1205 >> 61 X10Th.txt 4 3012291 3335299 10 >> 0.0708 >> 62 X10Th.txt 4 3353037 9459467 498 >> 0.6502 >> 63 X10Th.txt 4 9469402 9469402 3 >> -0.1167 >> 64 X10Th.txt 4 9473906 1.1E+07 123 >> 0.8942 >> 65 X10Th.txt 4 1.1E+07 1.4E+07 253 >> 0.334 >> 66 X10Th.txt 4 1.5E+07 1.6E+07 150 >> 0.8265 >> 67 X10Th.txt 4 1.6E+07 1.9E+07 179 >> 0.322 >> 68 X10Th.txt 4 1.9E+07 2.5E+07 463 >> 0.8283 >> 69 X10Th.txt 4 2.5E+07 2.5E+07 2 >> -4.1559 >> 70 X10Th.txt 4 2.5E+07 3.7E+07 759 >> 0.8149 >> 71 X10Th.txt 4 3.7E+07 3.7E+07 20 >> 1.2765 >> 72 X10Th.txt 4 3.7E+07 5.9E+07 1833 >> 0.4829 >> 73 X10Th.txt 4 5.9E+07 6E+07 83 1.0287 >> 74 X10Th.txt 4 6.0E+07 6.6E+07 455 >> 0.623 >> 75 X10Th.txt 4 6.6E+07 6.6E+07 3 >> -4.8121 >> 76 X10Th.txt 4 6.6E+07 8.7E+07 1509 >> 0.4519 >> 77 X10Th.txt 4 8.7E+07 8.8E+07 37 >> 0.9291 >> 78 X10Th.txt 4 8.8E+07 9.7E+07 764 >> 0.3171 >> 79 X10Th.txt 4 9.7E+07 1.0E+08 417 >> 0.8177 >> 80 X10Th.txt 4 1.0E+08 1.0E+08 35 >> 1.3066 >> 81 X10Th.txt 4 1.0E+08 1.1E+08 1125 >> 0.7607 >> 82 X10Th.txt 4 1.1E+08 1.2E+08 933 >> 0.3508 >> 83 X10Th.txt 4 1.2E+08 1.2E+08 192 >> 0.8091 >> 84 X10Th.txt 4 1.2E+08 1.2E+08 15 >> 1.3286 >> 85 X10Th.txt 4 1.2E+08 1.2E+08 78 >> 0.8328 >> 86 X10Th.txt 4 1.2E+08 1.4E+08 1514 >> 0.3228 >> 87 X10Th.txt 4 1.4E+08 1.4E+08 3 >> 1.2655 >> 88 X10Th.txt 4 1.4E+08 1.5E+08 1352 >> 0.283 >> 89 X10Th.txt 4 1.5E+08 1.5E+08 41 >> 0.8091 >> 90 X10Th.txt 4 1.5E+08 1.6E+08 793 >> 0.2844 >> 91 X10Th.txt 5 3003879 3.3E+07 2707 >> 0.105 >> 92 X10Th.txt 5 3.3E+07 3.3E+07 3 >> -0.6753 >> 93 X10Th.txt 5 3.3E+07 9.4E+07 5039 >> 0.1072 >> 94 X10Th.txt 5 9.4E+07 9.6E+07 8 >> -0.8031 >> 95 X10Th.txt 5 9.6E+07 1.5E+08 6236 >> 0.1028 >> 96 X10Th.txt 6 3024849 2.6E+07 1843 >> -0.1733 >> 97 X10Th.txt 6 2.6E+07 2.6E+07 2 >> -0.773 >> 98 X10Th.txt 6 2.6E+07 3.4E+07 864 >> -0.1393 >> 99 X10Th.txt 6 3.4E+07 3.4E+07 3 >> -2.5977 >> 100 X10Th.txt 6 3.4E+07 4.1E+07 744 >> -0.1363 >> 101 X10Th.txt 6 4.1E+07 4.1E+07 60 >> -0.9053 >> 102 X10Th.txt 6 4.1E+07 1.2E+08 7693 >> -0.1561 >> 103 X10Th.txt 6 1.2E+08 1.2E+08 2 >> 0.5483 >> 104 X10Th.txt 6 1.2E+08 1.5E+08 2924 >> -0.1333 >> 105 X10Th.txt 7 3049177 2.9E+07 2215 >> -0.174 >> 106 X10Th.txt 7 2.9E+07 2.9E+07 3 >> -0.8632 >> 107 X10Th.txt 7 2.9E+07 3.4E+07 496 >> -0.1613 >> 108 X10Th.txt 7 3.4E+07 3.5E+07 55 >> -0.6911 >> 109 X10Th.txt 7 3.5E+07 1.0E+08 6236 >> -0.1745 >> 110 X10Th.txt 7 1.0E+08 1.0E+08 5 >> -1.4229 >> 111 X10Th.txt 7 1.0E+08 1.0E+08 20 >> -0.1964 >> 112 X10Th.txt 7 1.0E+08 1.0E+08 6 >> -1.8286 >> 113 X10Th.txt 7 1.0E+08 1.5E+08 4582 >> -0.1627 >> 114 X10Th.txt 8 3111085 1.3E+08 >> 11524 -0.1437 >> 115 X10Th.txt 9 3088282 1.2E+08 >> 12045 0.2501 >> 116 X10Th.txt X 3086068 1.7E+08 >> 12085 -0.0107 >> 117 X10Th.txt Y 27 263780 52 -1.2383 >> 118 X10Th.txt Y 263932 631098 15 -0.5181 >> 119 X10Th.txt Y 631698 2177516 532 -1.256 >> 120 X11Th.txt 1 3002738 2.0E+08 >> 16394 -0.046 >> 121 X11Th.txt 10 3002742 2.2E+07 1710 >> -0.2582 >> 122 X11Th.txt 10 2.2E+07 2.2E+07 2 >> -2.3611 >> 123 X11Th.txt 10 2.2E+07 1.3E+08 >> 10121 -0.2586 >> 124 X11Th.txt 11 3026911 3.4E+07 2528 >> -0.049 >> 125 X11Th.txt 11 3.4E+07 3.4E+07 5 >> 1.0058 >> 126 X11Th.txt 11 3.4E+07 1.2E+08 >> 10125 -0.035 >> 127 X11Th.txt 12 3095298 6.3E+07 4424 >> -0.0904 >> 128 X11Th.txt 12 6.3E+07 6.3E+07 3 >> 1.7028 >> 129 X11Th.txt 12 6.3E+07 1.2E+08 5916 >> -0.0654 >> 130 X11Th.txt 13 3004789 1.3E+07 854 >> -0.1304 >> 131 X11Th.txt 13 1.3E+07 1.3E+07 5 >> -1.3861 >> 132 X11Th.txt 13 1.3E+07 2.8E+07 1591 >> -0.1782 >> 133 X11Th.txt 13 2.8E+07 2.8E+07 5 >> -1.3185 >> 134 X11Th.txt 13 2.8E+07 6.5E+07 3634 >> -0.1527 >> 135 X11Th.txt 13 6.6E+07 6.7E+07 8 >> -1.1874 >> 136 X11Th.txt 13 6.7E+07 6.9E+07 201 >> -0.1626 >> 137 X11Th.txt 13 6.9E+07 6.9E+07 4 >> 1.0844 >> 138 X11Th.txt 13 6.9E+07 1.2E+08 4340 >> -0.1625 >> 139 X11Th.txt 14 3892581 5.3E+07 4319 >> 0.6606 >> 140 X11Th.txt 14 5.3E+07 5.3E+07 58 >> -1.4906 >> 141 X11Th.txt 14 5.3E+07 1.2E+08 6310 >> 0.6554 >> 142 X11Th.txt 15 3091692 8039326 448 >> 0.4734 >> 143 X11Th.txt 15 8040778 8040778 3 >> 1.6185 >> 144 X11Th.txt 15 8046698 3.9E+07 2358 >> 0.454 >> 145 X11Th.txt 15 3.9E+07 3.9E+07 3 >> 1.5325 >> 146 X11Th.txt 15 3.9E+07 1.0E+08 6492 >> 0.4605 >> 147 X11Th.txt 16 3151162 9.8E+07 9041 >> -0.2314 >> 148 X11Th.txt 17 3009074 9.5E+07 9007 >> -0.0573 >> 149 X11Th.txt 18 3181133 9.1E+07 8058 >> 0.0341 >> 150 X11Th.txt 19 3147156 6.1E+07 6391 >> -0.1194 >> 151 X11Th.txt 2 3010301 5.0E+07 4560 >> 0.1442 >> 152 X11Th.txt 2 5.0E+07 5.0E+07 4 >> 1.1306 >> 153 X11Th.txt 2 5.0E+07 1.8E+08 >> 12292 0.1487 >> 154 X11Th.txt 3 3007185 6032558 245 >> -0.2823 >> 155 X11Th.txt 3 6056822 6072724 3 >> 1.2882 >> 156 X11Th.txt 3 6083291 1.6E+08 >> 12885 -0.2812 >> 157 X11Th.txt 4 3012291 3146483 5 >> -0.8101 >> 158 X11Th.txt 4 3159538 1.6E+08 >> 13637 0.2846 >> 159 X11Th.txt 5 3003879 1.1E+07 656 >> 0.0416 >> >> >> >> >> >> -- The Wellcome Trust Sanger Institute is operated by Genome >> Research >> Limited, a charity registered in England with number 1021457 and a >> company registered in England with number 2742969, whose >> registered office is 215 Euston Road, London, NW1 2BE. >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.**cond uctor<http: news.gmane.org="" gmane.science.biology.informatics.conducto="" r=""> >> >> >> > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, > a charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered offic...{{dropped:7}}
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