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 -- Sent via the guest posting facility at bioconductor.org.