[BioC] sort error in GRange
emily [guest]
guest at bioconductor.org
Tue Apr 30 20:37:11 CEST 2013
I have chip-seq data, and I would like to use GenomicRanges to count the overlap peaks. The files for the input are BED format generated from the peak calling. I used apply() function to generate bedlist, then I want to combine all those separate GRanges objects, each representing a single bed file, into a single big GRange object. I used do.call() function, then I would like to sort the chromosome location using sort() function, but it gave me an error as below.
> allorigins=sort(allorigins)
Error in x[!nas] : selecting spaces: subscript out of bounds
Could you please help me to fix this?
Thanks,
emily
-- output of sessionInfo():
> names(bedlist)=NULL
> allorigins=do.call(c, bedlist)
> allorigins=sort(allorigins)
Error in x[!nas] : selecting spaces: subscript out of bounds
> allorigins
RangedData with 258508 rows and 1 value column across 240 spaces
space ranges | name
<factor> <IRanges> | <character>
1 chr1 [ 564401, 570399] | 2726
2 chr1 [ 756001, 758799] | 76
3 chr1 [ 811201, 811799] | 34
4 chr1 [ 821801, 826199] | 43
5 chr1 [ 834801, 921999] | 2607
6 chr1 [ 928201, 942399] | 349
7 chr1 [ 944601, 951799] | 82
8 chr1 [ 955801, 1011599] | 2015
9 chr1 [1014001, 1029199] | 577
... ... ... ... ...
258500 chrX [153877201, 153891999] | 1427
258501 chrX [153955401, 153965999] | 806
258502 chrX [154002201, 154014399] | 1066
258503 chrY [ 9943601, 9944799] | 202
258504 chrY [ 9960801, 9968199] | 578
258505 chrY [ 9978601, 9990199] | 1543
258506 chrY [ 10005401, 10010399] | 502
258507 chrY [ 13458601, 13490199] | 12809
258508 chrY [ 59012201, 59020799] | 902
Warning messages:
1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels, :
duplicated levels will not be allowed in factors anymore
2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels, :
duplicated levels will not be allowed in factors anymore
> dim(allorigins)
[1] 258508 1
> allorigins[1:5,]
RangedData with 5 rows and 1 value column across 240 spaces
space ranges | name
<factor> <IRanges> | <character>
1 chr1 [564401, 570399] | 2726
2 chr1 [756001, 758799] | 76
3 chr1 [811201, 811799] | 34
4 chr1 [821801, 826199] | 43
5 chr1 [834801, 921999] | 2607
Warning message:
In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels, :
duplicated levels will not be allowed in factors anymore
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