Glad that it works :) btw, if you use seqlevels to control how many chromosome shown in the circular view, make sure every track data, have exactly the same seqlevels and seqlengths, order matters too, I don't have any validation now for different tracks ... I will add one later. cheers On Sat, May 3, 2014 at 9:15 PM, Miss Agnieszka Aleksandra Golicz < agnieszka.golicz@uq.net.au> wrote: > It worked. > > Thanks very much. > > I've never used GenomicRanges before trying ggbio this week and did not > realize one can add seqlevels like that. > > > Thanks again, your answer probably saved me lots of time! > > > Best wishes, > > Agnieszka > > > ------------------------------ > *From:* Tengfei Yin <tengfei.yin@sbgenomics.com> > *Sent:* 04 May 2014 11:03 > *To:* Miss Agnieszka Aleksandra Golicz > *Cc:* Hervé Pagès; vobencha@fhcrc.org; guest@bioconductor.org; > bioconductor@r-project.org; GenomicRanges Maintainer > *Subject:* Re: [BioC] [devteam-bioc] GenomicRanges seqlengths problem > > Hi Agnieszka, > > it's not really a ggbio related question, but would you mind try > > seqlevels(snps) <- names(seqlens) # then > seqlengths(snps) <- seqlens > > to see if that solved your problem. > > cheers > > Tengfei > > > > On Sat, May 3, 2014 at 6:32 PM, Miss Agnieszka Aleksandra Golicz < > agnieszka.golicz@uq.net.au> wrote: > >> Should I post it as a separate ggbio related questio? >> >> Best wishes, >> Agnieszka >> ________________________________________ >> From: Miss Agnieszka Aleksandra Golicz >> Sent: 02 May 2014 10:28 >> To: Hervé Pagès; vobencha@fhcrc.org; guest@bioconductor.org; >> bioconductor@r-project.org >> Cc: GenomicRanges Maintainer >> Subject: RE: [devteam-bioc] GenomicRanges seqlengths problem >> >> Sorry did not include my chromosome and snp files. >> >> It looks like this: >> chrs.txt - summary of chromosomes >> chr,start,end,len >> 0,1,4258568,4258568 >> 1,1,3378610,3378610 >> 2,1,2939989,2939989 >> 3,1,2348246,2348246 >> 4,1,1918205,1918205 >> 6,1,1888674,1888674 >> 5,1,1869450,1869450 >> 8,1,1809296,1809296 >> 9,1,1772623,1772623 >> 7,1,1769547,1769547 >> 10,1,1758670,1758670 >> 13,1,1634580,1634580 >> 12,1,1631710,1631710 >> 11,1,1590160,1590160 >> 15,1,1560629,1560629 >> 14,1,1533332,1533332 >> 17,1,1445693,1445693 >> 16,1,1397653,1397653 >> 18,1,1351976,1351976 >> 19,1,1186800,1186800 >> 20,1,1087932,1087932 >> 21,1,1020521,1020521 >> 22,1,731443,731443 >> 23,1,521426,521426 >> 24,1,475869,475869 >> 25,1,318058,318058 >> 26,1,261540,261540 >> 27,1,250629,250629 >> 28,1,236098,236098 >> 29,1,200940,200940 >> 30,1,154863,154863 >> 31,1,143268,143268 >> 32,1,87679,87679 >> 34,1,58596,58596 >> >> snps.txt - SNP file >> chr,id,start,end >> 6,egn4_Lema_G046740.1,538805,538805 >> 6,egn4_Lema_G049660.1,1607018,1607018 >> 10,egn4_Lema_G076370.1,1242542,1242542 >> 13,egn4_Lema_G081640.1,1352946,1352946 >> 12,egn4_Lema_G082370.1,109077,109077 >> 12,egn4_Lema_G085610.1,1190615,1190615 >> 12,egn4_Lema_G085620.1,1190933,1190933 >> 15,egn4_Lema_G090230.1,331669,331669 >> 16,egn4_Lema_G104510.1,667778,667778 >> 18,egn4_Lema_G110260.1,1321392,1321392 >> 19,egn4_Lema_G113060.1,958993,958993 >> 19,egn4_Lema_G113080.1,1177185,1177185 >> 21,egn4_Lema_G116710.1,263332,263332 >> >> If I only do that: >> dataChr <- read.table("chrs.txt",header=T,sep=",",stringsAsFactors=FALSE) >> dataChrS <- dataChr[order(dataChr$chr),] >> t <- read.table("snps.txt",header=T,sep=",") >> snps <- with(t, GRanges(chr, IRanges(start, end), id=id)) >> seqlens <- setNames(dataChrS$len, as.character(dataChrS$chr)) >> seqlengths(snps) <- seqlens >> I get the initial error - >> Error in .normargSeqlengths(value, seqnames(x)) : >> when the supplied 'seqlengths' vector is named, the names must match the >> seqnames >> Makes sense, there are no SNPs on some chromosomes >> >> If I do that: >> lChrs <- dataChrS[dataChrS$chr%in%t$chr,] >> seqlens <- setNames(lChrs$len, as.character(lChrs$chr)) >> seqlengths(snps) <- seqlens >> seqlegths(snps) >> 6 10 12 13 15 16 >> 1888674 1758670 1631710 1634580 1560629 1397653 >> >> I only have chromosomes with SNPs. >> >> Best wishes, >> Agnieszka >> >> ________________________________________ >> From: Miss Agnieszka Aleksandra Golicz >> Sent: 02 May 2014 10:01 >> To: Hervé Pagès; vobencha@fhcrc.org; guest@bioconductor.org; >> bioconductor@r-project.org >> Cc: GenomicRanges Maintainer >> Subject: RE: [devteam-bioc] GenomicRanges seqlengths problem >> >> Hello, >> >> Thank you very much for your help. >> >> I am facing one more problem with GRanges. >> I am trying to emulate this object. >> data("CRC", package = "biovizBase") >> object: mut.gr (it's SNP annotation for human chromosomes 1-22) >> >> When I just do show on mut.gr >> showmut.gr) >> GRanges with 60 ranges and 10 metadata columns: >> seqnames ranges strand | Hugo_Symbol >> Entrez_Gene_Id Center NCBI_Build Strand Variant_Classification >> Variant_Type Reference_Allele >> <rle> <iranges> <rle> | <factor> >> <integer> <factor> <integer> <factor> <factor> <factor> >> <factor> >> [1] 1 [ 11003085, 11003085] + | TARDBP >> 23435 Broad 36 + Missense SNP >> G >> [2] 1 [ 62352395, 62352395] + | INADL >> 10207 Broad 36 + Missense SNP >> T >> [3] 1 [194960885, 194960885] + | CFH >> 3075 Broad 36 + Missense SNP >> G >> [4] 2 [ 10116508, 10116508] - | CYS1 >> 192668 Broad 36 - Missense SNP >> C >> [5] 2 [ 33617747, 33617747] + | RASGRP3 >> 25780 Broad 36 + Missense SNP >> C >> [6] 2 [ 73894280, 73894280] + | C2orf78 >> 388960 Broad 36 + Missense SNP >> T >> [7] 2 [ 96732769, 96732769] + | FER1L5 >> 90342 Broad 36 + Missense SNP >> T >> [8] 2 [179160267, 179160267] - | TTN >> 7273 Broad 36 - Missense SNP >> C >> [9] 2 [217251189, 217251189] - | IGFBP5 >> 3488 Broad 36 - Missense SNP >> C >> [10] 3 [ 12620699, 12620699] - | RAF1 >> 5894 Broad 36 - Missense SNP >> G >> [11] 3 [ 46472880, 46472880] - | LTF >> 4057 Broad 36 - Missense SNP >> C >> [12] 3 [137203130, 137203130] + | PPP2R3A >> 5523 Broad 36 + Missense SNP >> A >> [13] 3 [137457429, 137457429] + | PCCB >> 5096 Broad 36 + Missense SNP >> C >> [14] 3 [184708629, 184708629] - | KLHL6 >> 89857 Broad 36 - Missense SNP >> G >> [15] 4 [147434591, 147434591] - | SLC10A7 >> 84068 Broad 36 - Missense SNP >> G >> [16] 4 [185915412, 185915412] - | ACSL1 >> 2180 Broad 36 - Missense SNP >> A >> [17] 5 [ 79070342, 79070342] + | CMYA5 >> 202333 Broad 36 + Missense SNP >> C >> [18] 5 [ 94775579, 94775579] + | FAM81B >> 153643 Broad 36 + Missense SNP >> G >> [19] 5 [140838266, 140838266] + | PCDHGC3 >> 5098 Broad 36 + Missense SNP >> T >> [20] 6 [109992724, 109992724] - | AKD1 >> 221264 Broad 36 - Missense SNP >> C >> [21] 6 [118993492, 118993492] - | C6orf204 >> 387119 Broad 36 - Missense SNP >> G >> [22] 7 [124286401, 124286401] - | POT1 >> 25913 Broad 36 - Missense SNP >> A >> [23] 7 [125960456, 125960456] - | GRM8 >> 2918 Broad 36 - Missense SNP >> A >> [24] 9 [ 35097658, 35097658] - | KIAA1539 >> 80256 Broad 36 - Missense SNP >> A >> [25] 9 [103164773, 103164773] - | BAAT >> 570 Broad 36 - Missense SNP >> G >> [26] 9 [132745783, 132745783] + | ABL1 >> 25 Broad 36 + Missense SNP >> C >> [27] 9 [138481305, 138481305] - | SEC16A >> 9919 Broad 36 - Missense SNP >> C >> [28] 10 [ 7661761, 7661761] - | ITIH5 >> 80760 Broad 36 - Missense SNP >> C >> [29] 10 [106064683, 106064683] - | ITPRIP >> 85450 Broad 36 - Missense SNP >> T >> [30] 11 [ 603430, 603430] - | IRF7 >> 3665 Broad 36 - Missense SNP >> G >> [31] 11 [ 5610148, 5610148] + | TRIM34 >> 53840 Broad 36 + Missense SNP >> A >> [32] 11 [ 9420281, 9420281] + | IPO7 >> 10527 Broad 36 + Missense SNP >> G >> [33] 11 [ 26495005, 26495005] + | ANO3 >> 63982 Broad 36 + Missense SNP >> C >> [34] 11 [ 55629818, 55629818] + | OR8H2 >> 390151 Broad 36 + Missense SNP >> G >> [35] 11 [116737834, 116737834] + | CEP164 >> 22897 Broad 36 + Missense SNP >> C >> [36] 12 [ 25165980, 25165980] - | CASC1 >> 55259 Broad 36 - Missense SNP >> G >> [37] 12 [ 25289548, 25289548] - | KRAS >> 3845 Broad 36 - Missense SNP >> C >> [38] 12 [ 31142142, 31142142] + | DDX11 >> 1663 Broad 36 + Missense SNP >> G >> [39] 12 [ 42434771, 42434771] - | PUS7L >> 83448 Broad 36 - Missense SNP >> T >> [40] 12 [ 55006974, 55006974] - | PAN2 >> 9924 Broad 36 - Missense SNP >> T >> [41] 13 [102199348, 102199348] - | LOC643677 >> 643677 Broad 36 - Missense SNP >> G >> [42] 15 [ 40503502, 40503502] - | ZFP106 >> 64397 Broad 36 - Missense SNP >> C >> [43] 15 [ 70816269, 70816269] + | BBS4 >> 585 Broad 36 + Missense SNP >> A >> [44] 16 [ 23481033, 23481033] + | UBFD1 >> 56061 Broad 36 + Missense SNP >> C >> [45] 17 [ 21149010, 21149010] + | MAP2K3 >> 5606 Broad 36 + Missense SNP >> G >> [46] 17 [ 35812691, 35812691] - | TOP2A >> 7153 Broad 36 - Missense SNP >> T >> [47] 18 [ 16788810, 16788810] - | ROCK1 >> 6093 Broad 36 - Missense SNP >> C >> [48] 18 [ 75322338, 75322338] + | NFATC1 >> 4772 Broad 36 + Missense SNP >> G >> [49] 19 [ 15713495, 15713495] + | OR10H3 >> 26532 Broad 36 + Missense SNP >> G >> [50] 19 [ 40730140, 40730140] + | TMEM147 >> 10430 Broad 36 + Missense SNP >> C >> [51] 19 [ 52338664, 52338664] + | SAE1 >> 10055 Broad 36 + Missense SNP >> G >> [52] 19 [ 57407795, 57407795] + | PPP2R1A >> 5518 Broad 36 + Missense SNP >> G >> [53] 20 [ 23298287, 23298287] + | GZF1 >> 64412 Broad 36 + Missense SNP >> A >> [54] 20 [ 31012946, 31012946] + | EFCAB8 >> 388795 Broad 36 + Missense SNP >> C >> [55] 20 [ 40223536, 40223536] - | PTPRT >> 11122 Broad 36 - Missense SNP >> C >> [56] 20 [ 54467136, 54467136] + | CASS4 >> 57091 Broad 36 + Missense SNP >> G >> [57] 20 [ 60201983, 60201983] + | GTPBP5 >> 26164 Broad 36 + Missense SNP >> C >> [58] 21 [ 36688774, 36688774] + | CHAF1B >> 8208 Broad 36 + Missense SNP >> C >> [59] 21 [ 39699770, 39699770] - | LCA5L >> 150082 Broad 36 - Missense SNP >> T >> [60] 22 [ 27437953, 27437953] - | CHEK2 >> 11200 Broad 36 - Missense SNP >> C >> >> In the seqnames column chromosomes 8 and 14 are missing, which makes >> sense - there is no SNPs on those. >> >> However, when do: >> head(seqlengthsmut.gr), 25) >> >> 1 2 3 4 5 6 7 >> 8 9 10 11 12 13 14 15 >> 249250621 243199373 198022430 191154276 180915260 171115067 159138663 >> 146364022 141213431 135534747 135006516 133851895 115169878 107349540 >> 102531392 >> 16 17 18 19 20 21 22 >> 90354753 81195210 78077248 59128983 63025520 48129895 51304566 >> >> All 22 chromosomes are there. >> >> How is that possible? >> >> I believe that for my data, I need to do a similar thing (I'm trying to >> create a multilayer circular plot in ggbio). Although I have snps for only >> few chromosomes, I think I need to include lengths for all of them. >> How do I do that? >> >> Best wishes, >> Agnieszka >> ________________________________________ >> From: Hervé Pagès <hpages@fhcrc.org> >> Sent: 02 May 2014 03:27 >> To: vobencha@fhcrc.org; guest@bioconductor.org; >> bioconductor@r-project.org; Miss Agnieszka Aleksandra Golicz >> Cc: GenomicRanges Maintainer >> Subject: Re: [devteam-bioc] GenomicRanges seqlengths problem >> >> On 05/01/2014 10:21 AM, Maintainer wrote: >> > Hi Sonia, Val, >> > >> > On 05/01/2014 09:52 AM, Maintainer wrote: >> >> Hi, >> >> >> >> The seqnames are in a different orders in the 'chrs' and 'sl' objects. >> >> Looking at the first 3 names in each, >> >> >> >> > head(seqlengths(chrs), 3) >> >> lm_SuperContig_0_v2 lm_SuperContig_1_v2 lm_SuperContig_10_v2 >> >> NA NA NA >> >> >> >> > head(sl, 3) >> >> lm_SuperContig_0_v2 lm_SuperContig_1_v2 lm_SuperContig_2_v2 >> >> 4258568 3378610 2939989 >> >> >> >> When a GRanges is created, seqnames are sorted in ascii order. >> > >> > Just to clarify, the seqlevels are sorted, not the seqnames: >> > >> > > gr <- GRanges(c("b", "a", "b"), IRanges(1:3, 10)) >> > > gr >> > GRanges with 3 ranges and 0 metadata columns: >> > seqnames ranges strand >> > <rle> <iranges> <rle> >> > [1] b [1, 10] * >> > [2] a [2, 10] * >> > [3] b [3, 10] * >> > --- >> > seqlengths: >> > a b >> > NA NA >> > >> > Not sorted (i.e. user-supplied order is preserved): >> > >> > > seqnames(gr) >> > factor-Rle of length 3 with 3 runs >> > Lengths: 1 1 1 >> > Values : b a b >> > Levels(2): a b >> > >> > Sorted: >> > >> > > seqlevels(gr) >> > [1] "a" "b" >> > >> > This sorting of the seqlevels is not good anyway (people with different >> > LOCALE will get different results). I just fixed this so now the >> > GRanges() constructor will preserve the seqlevels in the order supplied >> > by the user: >> > >> > > gr <- GRanges(c("b", "a", "b"), IRanges(1:3, 10)) >> > > seqlevels(gr) >> > [1] "b" "a" >> > >> > More precisely, the seqlevels are obtained by doing unique() on the >> > seqnames. >> > >> > The fix will propagate to the public repos and become available thru >> > biocLite() in the next 24 hours. >> > >> > Then your original code should just work Sonia. >> >> Or maybe not :) You might still need to use 'stringsAsFactors=FALSE' >> when calling read.table(). Please let us know if that still doesn't >> make it. >> >> Thanks, >> H. >> >> > >> > Cheers, >> > H. >> > >> > >> >> You can >> >> see the full list with seqinfo(): >> >> >> >> > seqinfo(chrs) >> >> Seqinfo of length 34 >> >> seqnames seqlengths isCircular genome >> >> lm_SuperContig_0_v2 <na> <na> <na> >> >> lm_SuperContig_1_v2 <na> <na> <na> >> >> lm_SuperContig_10_v2 <na> <na> <na> >> >> lm_SuperContig_11_v2 <na> <na> <na> >> >> lm_SuperContig_12_v2 <na> <na> <na> >> >> ... ... ... ... >> >> >> >> The seqnames in the replacement vector must match the order in the >> >> 'Seqinfo' object. >> >> >> >> To re-order: >> >> >> >> sl_new <- sl[match(levels(factor(names(sl))), names(sl))] >> >> >> >> Then add the new lengths: >> >> >> >>>> seqlengths(chrs) <- sl_new >> >>>> chrs >> >>> GRanges with 34 ranges and 0 metadata columns: >> >>> seqnames ranges strand >> >>> <rle> <iranges> <rle> >> >>> [1] lm_SuperContig_0_v2 [1, 4258568] * >> >>> [2] lm_SuperContig_1_v2 [1, 3378610] * >> >>> [3] lm_SuperContig_2_v2 [1, 2939989] * >> >>> [4] lm_SuperContig_3_v2 [1, 2348246] * >> >>> [5] lm_SuperContig_4_v2 [1, 1918205] * >> >>> ... ... ... ... >> >>> [30] lm_SuperContig_29_v2 [1, 200940] * >> >>> [31] lm_SuperContig_30_v2 [1, 154863] * >> >>> [32] lm_SuperContig_31_v2 [1, 143268] * >> >>> [33] lm_SuperContig_32_v2 [1, 87679] * >> >>> [34] lm_SuperContig_34_v2 [1, 58596] * >> >>> --- >> >>> seqlengths: >> >>> lm_SuperContig_0_v2 lm_SuperContig_1_v2 ... >> lm_SuperContig_9_v2 >> >>> 4258568 3378610 ... >> 1772623 >> >> >> >> >> >> Valerie >> >> >> >> >> >> On 05/01/2014 07:20 AM, Maintainer wrote: >> >>> >> >>> Hello, >> >>> >> >>> I have a problem with supplying GRanges object with seqlengths. >> >>> I have a files. >> >>> chrs.txt - contains information about chromosomes >> >>> >> >>> chrs.txt >> >>> chr,start,end,len >> >>> lm_SuperContig_0_v2,1,4258568,4258568 >> >>> lm_SuperContig_1_v2,1,3378610,3378610 >> >>> lm_SuperContig_2_v2,1,2939989,2939989 >> >>> lm_SuperContig_3_v2,1,2348246,2348246 >> >>> lm_SuperContig_4_v2,1,1918205,1918205 >> >>> lm_SuperContig_6_v2,1,1888674,1888674 >> >>> lm_SuperContig_5_v2,1,1869450,1869450 >> >>> lm_SuperContig_8_v2,1,1809296,1809296 >> >>> lm_SuperContig_9_v2,1,1772623,1772623 >> >>> lm_SuperContig_7_v2,1,1769547,1769547 >> >>> lm_SuperContig_10_v2,1,1758670,1758670 >> >>> lm_SuperContig_13_v2,1,1634580,1634580 >> >>> lm_SuperContig_12_v2,1,1631710,1631710 >> >>> lm_SuperContig_11_v2,1,1590160,1590160 >> >>> lm_SuperContig_15_v2,1,1560629,1560629 >> >>> lm_SuperContig_14_v2,1,1533332,1533332 >> >>> lm_SuperContig_17_v2,1,1445693,1445693 >> >>> lm_SuperContig_16_v2,1,1397653,1397653 >> >>> lm_SuperContig_18_v2,1,1351976,1351976 >> >>> lm_SuperContig_19_v2,1,1186800,1186800 >> >>> lm_SuperContig_20_v2,1,1087932,1087932 >> >>> lm_SuperContig_21_v2,1,1020521,1020521 >> >>> lm_SuperContig_22_v2,1,731443,731443 >> >>> lm_SuperContig_23_v2,1,521426,521426 >> >>> lm_SuperContig_24_v2,1,475869,475869 >> >>> lm_SuperContig_25_v2,1,318058,318058 >> >>> lm_SuperContig_26_v2,1,261540,261540 >> >>> lm_SuperContig_27_v2,1,250629,250629 >> >>> lm_SuperContig_28_v2,1,236098,236098 >> >>> lm_SuperContig_29_v2,1,200940,200940 >> >>> lm_SuperContig_30_v2,1,154863,154863 >> >>> lm_SuperContig_31_v2,1,143268,143268 >> >>> lm_SuperContig_32_v2,1,87679,87679 >> >>> lm_SuperContig_34_v2,1,58596,58596 >> >>> >> >>> I try to do the following: >> >>> # creating GRanges object for chromosomes >> >>> dataChr <- read.table("chrs.txt",header=T,sep=",") >> >>> chrs <- with(dataChr, GRanges(chr, IRanges(start, end))) >> >>> sl <- setNames(dataChr$len, as.character(dataChr$chr)) >> >>> seqlengths(chrs) <- sl >> >>> >> >>> And I get the following error: >> >>> >> >>> Error in .normargSeqlengths(value, seqnames(x)) : >> >>> when the supplied 'seqlengths' vector is named, the names must >> match the seqnames >> >>> >> >>> Any chance you could help me with what is going on? >> >>> >> >>> Best wishes, >> >>> Agnieszka >> >>> >> >>> >> >>> -- output of sessionInfo(): >> >>> >> >>> R version 3.1.0 (2014-04-10) >> >>> Platform: i386-w64-mingw32/i386 (32-bit) >> >>> >> >>> locale: >> >>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 >> >>> [4] LC_NUMERIC=C LC_TIME=English_United >> Kingdom.1252 >> >>> >> >>> attached base packages: >> >>> [1] parallel stats graphics grDevices utils datasets >> methods base >> >>> >> >>> other attached packages: >> >>> [1] XVector_0.4.0 ggbio_1.12.3 ggplot2_0.9.3.1 >> GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 IRanges_1.22.4 >> BiocGenerics_0.10.0 >> >>> [8] BiocInstaller_1.14.2 >> >>> >> >>> loaded via a namespace (and not attached): >> >>> [1] AnnotationDbi_1.26.0 BatchJobs_1.2 BBmisc_1.6 >> Biobase_2.24.0 BiocParallel_0.6.0 >> biomaRt_2.20.0 >> >>> [7] Biostrings_2.32.0 biovizBase_1.12.1 >> bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 >> cluster_1.15.2 >> >>> [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> dichromat_2.0-0 digest_0.6.4 fail_1.2 >> >>> [19] foreach_1.4.2 Formula_1.1-1 >> GenomicAlignments_1.0.0 GenomicFeatures_1.16.0 grid_3.1.0 >> gridExtra_0.9.1 >> >>> [25] gtable_0.1.2 Hmisc_3.14-4 >> iterators_1.0.7 labeling_0.2 lattice_0.20-29 >> latticeExtra_0.6-26 >> >>> [31] MASS_7.3-31 munsell_0.4.2 plyr_1.8.1 >> proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> >>> [37] RCurl_1.95-4.1 reshape2_1.4 >> Rsamtools_1.16.0 RSQLite_0.11.4 rtracklayer_1.24.0 >> scales_0.2.4 >> >>> [43] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 >> stringr_0.6.2 survival_2.37-7 tools_3.1.0 >> >>> [49] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >> >>> >> >>> >> >>> -- >> >>> Sent via the guest posting facility at bioconductor.org. >> >>> >> >>> >> ___________________________________________________________________ _____ >> >>> devteam-bioc mailing list >> >>> To unsubscribe from this mailing list send a blank email to >> >>> devteam-bioc-leave@lists.fhcrc.org >> >>> You can also unsubscribe or change your personal options at >> >>> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >> >>> >> >> >> >> >> > >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages@fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> 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 >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]