Hello, I am trying to append together two GRangesLists. I thought that either c() or append would allow me to do this, but I'm getting an error. My two GRangesLists have the same metadata column names. With both, I'm getting some kind of error about rownames that I don't understand and I just don't have any ideas about trying to track this down. My system information is below (R 2.11.1, GenomicRanges_1.0.9). Thanks for any help, Elizabeth #my two GRangesList > disjointElementsCds GRangesList of length 44 $100132288 GRanges with 6 ranges and 1 elementMetadata value seqnames ranges strand | disjEx_id <rle> <iranges> <rle> | <integer> [1] chr21_random [103280, 104416] * | 1 [2] chr21_random [104417, 104518] * | 2 [3] chr21_random [105133, 105363] * | 3 [4] chr21_random [162407, 162463] * | 4 [5] chr21_random [162464, 162465] * | 5 [6] chr21_random [164601, 164670] * | 6 ... <43 more elements> seqlengths chr1 chr1_random chr10 chr10_random chr11 ... chr9_random chrM chrX chrX_random chrY 247249719 1663265 135374737 113275 134452384 ... 1146434 16571 154913754 1719168 57772954 > disjointElementsNonCds GRangesList of length 7 $152687 GRanges with 6 ranges and 1 elementMetadata value seqnames ranges strand | disjEx_id <rle> <iranges> <rle> | <integer> [1] chr4 [ 43227, 43385] * | 1 [2] chr4 [ 49323, 49449] * | 2 [3] chr4 [ 49951, 50046] * | 3 [4] chr4 [ 57732, 58380] * | 4 [5] chr4 [184870, 185000] * | 5 [6] chr4 [185421, 186092] * | 6 $26751 GRanges with 8 ranges and 1 elementMetadata value seqnames ranges strand | disjEx_id <rle> <iranges> <rle> | <integer> [1] chr2 [208155, 209001] * | 1 [2] chr2 [214864, 214920] * | 2 [3] chr2 [219966, 220044] * | 3 [4] chr2 [221023, 221191] * | 4 [5] chr2 [223101, 223229] * | 5 [6] chr2 [224160, 224272] * | 6 [7] chr2 [237538, 237602] * | 7 [8] chr2 [239731, 239852] * | 8 $403340 GRanges with 1 range and 1 elementMetadata value seqnames ranges strand | disjEx_id <rle> <iranges> <rle> | <integer> [1] chr17_random [116623, 119732] * | 1 ... <4 more elements> seqlengths chr1 chr1_random chr10 chr10_random chr11 ... chr9_random chrM chrX chrX_random chrY 247249719 1663265 135374737 113275 134452384 ... 1146434 16571 154913754 1719168 57772954 #my attempt to join them together > disjointElements<-append(disjointElementsCds,values=disjointElementsNo nCds) Error in `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771", : invalid rownames length > disjointElements<-c(disjointElementsCds,values=disjointElementsNonCds) Error in `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771", : invalid rownames length > traceback() 9: stop("invalid rownames length") 8: `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771", "114821", "123887", "133957", "140850", "153478", "23192", "245938", "255403", "283768", "283897", "3081", "3166", "335", "347688", "3662", "375690", "375791", "3803", "3810", "389257", "404785", "440073", "440153", "441308", "51078", "55344", "56900", "56940", "5987", "642273", "643836", "6942", "7179", "727800", "81623", "83482", "83755", "8694", "9097", "92259", "9501", "152687", "26751", "403340", "644128", "645520", "64946", "653635")) 7: `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771", "114821", "123887", "133957", "140850", "153478", "23192", "245938", "255403", "283768", "283897", "3081", "3166", "335", "347688", "3662", "375690", "375791", "3803", "3810", "389257", "404785", "440073", "440153", "441308", "51078", "55344", "56900", "56940", "5987", "642273", "643836", "6942", "7179", "727800", "81623", "83482", "83755", "8694", "9097", "92259", "9501", "152687", "26751", "403340", "644128", "645520", "64946", "653635")) 6: .local(x, ...) 5: elementMetadata(x) 4: elementMetadata(x) 3: .c.Sequence(x, ...) 2: c(disjointElementsCds, values = disjointElementsNonCds) 1: c(disjointElementsCds, values = disjointElementsNonCds) > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] graph_1.26.0 projectManager_1.0 XML_3.1-1 GenomicFeatures_1.0.10 GenomicRanges_1.0.9 IRanges_1.6.16 loaded via a namespace (and not attached): [1] Biobase_2.8.0 biomaRt_2.4.0 Biostrings_2.16.9 BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-2 RSQLite_0.9-2 rtracklayer_1.8.1 [9] tools_2.11.1

Hi Elizabeth -- This does seem to be a bug in IRanges; a reproducible example is just example(GRangesList) c(grl, grl) A work around is to remove and reapply the 'names', e.g., cc <- function(...) { args <- list(...) names <- unlist(lapply(args, names)) result <- do.call(c, args) names(result) <- names result } This appears not to be a problem in the development version, e.g., > sessionInfo() R version 2.12.0 Under development (unstable) (2010-09-05 r52874) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.1.25 IRanges_1.7.32 loaded via a namespace (and not attached): [1] tools_2.12.0 Martin On 09/10/2010 12:43 PM, Elizabeth Purdom wrote: > Hello, > I am trying to append together two GRangesLists. I thought that either > c() or append would allow me to do this, but I'm getting an error. My > two GRangesLists have the same metadata column names. With both, I'm > getting some kind of error about rownames that I don't understand and > I just don't have any ideas about trying to track this down. My system > information is below (R 2.11.1, GenomicRanges_1.0.9). > Thanks for any help, > Elizabeth > > #my two GRangesList > > disjointElementsCds > GRangesList of length 44 > $100132288 > GRanges with 6 ranges and 1 elementMetadata value > seqnames ranges strand | disjEx_id > <rle> <iranges> <rle> | <integer> > [1] chr21_random [103280, 104416] * | 1 > [2] chr21_random [104417, 104518] * | 2 > [3] chr21_random [105133, 105363] * | 3 > [4] chr21_random [162407, 162463] * | 4 > [5] chr21_random [162464, 162465] * | 5 > [6] chr21_random [164601, 164670] * | 6 > > ... > <43 more elements> > > > seqlengths > chr1 chr1_random chr10 chr10_random chr11 > ... chr9_random chrM chrX chrX_random chrY > 247249719 1663265 135374737 113275 134452384 > ... 1146434 16571 154913754 1719168 57772954 > > > disjointElementsNonCds > GRangesList of length 7 > $152687 > GRanges with 6 ranges and 1 elementMetadata value > seqnames ranges strand | disjEx_id > <rle> <iranges> <rle> | <integer> > [1] chr4 [ 43227, 43385] * | 1 > [2] chr4 [ 49323, 49449] * | 2 > [3] chr4 [ 49951, 50046] * | 3 > [4] chr4 [ 57732, 58380] * | 4 > [5] chr4 [184870, 185000] * | 5 > [6] chr4 [185421, 186092] * | 6 > > $26751 > GRanges with 8 ranges and 1 elementMetadata value > seqnames ranges strand | disjEx_id > <rle> <iranges> <rle> | <integer> > [1] chr2 [208155, 209001] * | 1 > [2] chr2 [214864, 214920] * | 2 > [3] chr2 [219966, 220044] * | 3 > [4] chr2 [221023, 221191] * | 4 > [5] chr2 [223101, 223229] * | 5 > [6] chr2 [224160, 224272] * | 6 > [7] chr2 [237538, 237602] * | 7 > [8] chr2 [239731, 239852] * | 8 > > $403340 > GRanges with 1 range and 1 elementMetadata value > seqnames ranges strand | disjEx_id > <rle> <iranges> <rle> | <integer> > [1] chr17_random [116623, 119732] * | 1 > > ... > <4 more elements> > > > seqlengths > chr1 chr1_random chr10 chr10_random chr11 > ... chr9_random chrM chrX chrX_random chrY > 247249719 1663265 135374737 113275 134452384 > ... 1146434 16571 154913754 1719168 57772954 > > #my attempt to join them together > > > disjointElements<-append(disjointElementsCds,values=disjointElements NonCds) > > Error in `rownames<-`(`*tmp*`, value = c("100132288", "10752", > "10771", : > invalid rownames length > > disjointElements<-c(disjointElementsCds,values=disjointElementsNonCds) > Error in `rownames<-`(`*tmp*`, value = c("100132288", "10752", > "10771", : > invalid rownames length > > traceback() > 9: stop("invalid rownames length") > 8: `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771", > "114821", "123887", "133957", "140850", "153478", "23192", "245938", > "255403", "283768", "283897", "3081", "3166", "335", "347688", > "3662", "375690", "375791", "3803", "3810", "389257", "404785", > "440073", "440153", "441308", "51078", "55344", "56900", "56940", > "5987", "642273", "643836", "6942", "7179", "727800", "81623", > "83482", "83755", "8694", "9097", "92259", "9501", "152687", > "26751", "403340", "644128", "645520", "64946", "653635")) > 7: `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771", > "114821", "123887", "133957", "140850", "153478", "23192", "245938", > "255403", "283768", "283897", "3081", "3166", "335", "347688", > "3662", "375690", "375791", "3803", "3810", "389257", "404785", > "440073", "440153", "441308", "51078", "55344", "56900", "56940", > "5987", "642273", "643836", "6942", "7179", "727800", "81623", > "83482", "83755", "8694", "9097", "92259", "9501", "152687", > "26751", "403340", "644128", "645520", "64946", "653635")) > 6: .local(x, ...) > 5: elementMetadata(x) > 4: elementMetadata(x) > 3: .c.Sequence(x, ...) > 2: c(disjointElementsCds, values = disjointElementsNonCds) > 1: c(disjointElementsCds, values = disjointElementsNonCds) > > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] graph_1.26.0 projectManager_1.0 > XML_3.1-1 GenomicFeatures_1.0.10 GenomicRanges_1.0.9 > IRanges_1.6.16 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 biomaRt_2.4.0 Biostrings_2.16.9 > BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-2 > RSQLite_0.9-2 rtracklayer_1.8.1 > [9] tools_2.11.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor