Entering edit mode
Hi,
I'm having problems using the seqlengths parameter. Suggestions ?
> head(x)
chr position
1 chr12 13352230
2 chr11 66387388
3 chr16 54958470
4 chr16 54901876
5 chr11 66386240
6 chr16 54925044
sequence
1 CAGAGACCAGATTAGGCCCATCAAGTTCCCAGCCTTGTCAGTGGGCTTCA
2 AGATAGGAGAACTTGTTTTTCTGGATTCACTTAACTTTGTTACTGGAGGACTTG
3 TCTTTCTCATAGCTTTTCTTACCTGCCTATATTCAGCAGCCTCTATTTGATGAGAAATGACAAG
4 AGTATTAAACAAGAATGCACGTAAAGTGTGCAATGCATATAGCAGACAGTCAAGAAATGGTGT
5 CAAACATCTGAAGGGACAGTCTCCCTGGAACTCAGGCTTCTTGCTGGCTT
6 AGGAAAGTTTCCCAGGTTTCATTACATGTTTTCACGATTTAGCTTAAATGTT
> seqlengths(Hsapiens)[unique(x$chr)]
chr4 chr3 chr7 chr8 chr15 chr18 chr10
chr5
191154276 198022430 159138663 146364022 102531392 78077248 135534747
180915260
chr17 chr11 chr2 chr20 chr21 chr6 chr19
chrX
81195210 135006516 243199373 63025520 48129895 171115067 59128983
155270560
chr22 chr1 chr16 chr12 chr9 chr14 chr13
51304566 249250621 90354753 133851895 141213431 107349540 115169878
> GRanges(x$chr, IRanges(x$position, width=1),
seqlengths=seqlengths(Hsapiens)[unique(x$chr)])
Error in validObject(.Object) :
invalid class ?GRanges?object: 'seqnames' contains missing values
> GRanges(x$chr, IRanges(x$position, width=1))
GRanges with 59335 ranges and 0 elementMetadata cols:
seqnames ranges strand
<rle> <iranges> <rle>
[1] chr12 [13352230, 13352230] *
[2] chr11 [66387388, 66387388] *
[3] chr16 [54958470, 54958470] *
[4] chr16 [54901876, 54901876] *
[5] chr11 [66386240, 66386240] *
[6] chr16 [54925044, 54925044] *
[7] chr12 [88888128, 88888128] *
[8] chr11 [ 1075886, 1075886] *
[9] chr16 [54893488, 54893488] *
... ... ... ...
[59327] chr8 [ 82392570, 82392570] *
[59328] chr3 [195474810, 195474810] *
[59329] chr1 [ 77335014, 77335014] *
[59330] chr4 [141674200, 141674200] *
[59331] chr5 [176021996, 176021996] *
[59332] chr16 [ 54931950, 54931950] *
[59333] chr16 [ 54960706, 54960706] *
[59334] chr5 [150321696, 150321696] *
[59335] chr19 [ 33791323, 33791323] *
---
seqlengths:
chr1 chr10 chr11 chr12 chr14 chr15 ... chr6 chr7 chr8 chr9
chrX chrY
NA NA NA NA NA NA ... NA NA NA NA
NA NA
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.17 BSgenome_1.24.0
[3] Biostrings_2.24.1 GenomicRanges_1.8.6
[5] IRanges_1.14.2 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] stats4_2.15.0
