Hi all, I seem to be getting an error message on trying to use rbind() on two relatively innocuous-looking RangedData objects - see below. I was wondering if anyone else has had the same problem. This works fine on simpler objects, so my guess would be that these particular objects are malformed in some way but I'm not sure how I would check that. I can get around this by manually coercing each RangedData object to a data.frame, but that approach seems suboptimal to me. Thanks, Jonathan -------- > a RangedData with 3032 rows and 0 value columns across 25 spaces space ranges | <character> <iranges> | 1 chr1 [1274369, 1274619] | 2 chr1 [1310219, 1310569] | 3 chr1 [1907419, 1907769] | 4 chr1 [1983269, 1983469] | 5 chr1 [2355219, 2355319] | 6 chr1 [2431369, 2432219] | 7 chr1 [2446219, 2446619] | 8 chr1 [3441819, 3442169] | 9 chr1 [3657769, 3657919] | ... ... ... ... 3024 chrX [106724271, 106724371] | 3025 chrX [106983671, 106983771] | 3026 chrX [108586171, 108586271] | 3027 chrX [108781571, 108781671] | 3028 chrX [110424871, 110425571] | 3029 chrX [152256221, 152256371] | 3030 chrX [152619071, 152619221] | 3031 chrX [152661471, 152662221] | 3032 chrX [152662571, 152662671] | > names(a) ##n.b. no ranges present for space "chrM" [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" [10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5" [19] "chr6" "chr7" "chr8" "chr9" "chrM" "chrX" "chrY" > b RangedData with 6486 rows and 0 value columns across 23 spaces space ranges | <character> <iranges> | 1 chr1 [1274159, 1274912] | 2 chr1 [1309807, 1310770] | 3 chr1 [1532507, 1532754] | 4 chr1 [1907180, 1907982] | 5 chr1 [1983127, 1983848] | 6 chr1 [2354988, 2355437] | 7 chr1 [2431031, 2432299] | 8 chr1 [2433599, 2433985] | 9 chr1 [2446015, 2446750] | ... ... ... ... 6478 chrX [152618904, 152619429] | 6479 chrX [152660747, 152661246] | 6480 chrX [152661264, 152662298] | 6481 chrX [152662420, 152662899] | 6482 chrX [152664180, 152664467] | 6483 chrX [152665288, 152665502] | 6484 chrX [152758426, 152758742] | 6485 chrX [153591715, 153591957] | 6486 chrX [153849434, 153849749] | > names(b) ## (chrY, chrM not present in this object) [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" [10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5" [19] "chr6" "chr7" "chr8" "chr9" "chrX" > rbind(a,b) Error in .Method(..., deparse.level = deparse.level) : column names for arg 23 do not match those of first arg > traceback() 17: stop("column names for arg ", i, " do not match those of first arg") 16: .Method(..., deparse.level = deparse.level) 15: eval(expr, envir, enclos) 14: eval(.dotsCall, env) 13: eval(.dotsCall, env) 12: standardGeneric("rbind") 11: function (..., deparse.level = 1) standardGeneric("rbind")(<s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">) 10: do.call(rbind, unname(x)) 9: .compress.list(lapply(unlistData, as, elementTypeData)) 8: newCompressedList("CompressedSplitDataFrameList", listData) 7: SplitDataFrameList(do.call(Map, c(list(safe.rbind), dfs))) 6: .Method(..., deparse.level = deparse.level) 5: eval(expr, envir, enclos) 4: eval(.dotsCall, env) 3: eval(.dotsCall, env) 2: standardGeneric("rbind") 1: rbind(a, b) > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.10.0 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.2 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0 [4] GenomicRanges_1.2.1 tools_2.12.0 XML_3.2-0 This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. 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Hi Jonathan, Could you please send me a simple reproducible example? I think I've fixed this, but I can't really be sure. Thanks, Michael On Wed, Nov 24, 2010 at 6:09 AM, Jonathan Cairns < Jonathan.Cairns@cancer.org.uk> wrote: > Hi all, > > I seem to be getting an error message on trying to use rbind() on two > relatively innocuous-looking RangedData objects - see below. I was wondering > if anyone else has had the same problem. This works fine on simpler objects, > so my guess would be that these particular objects are malformed in some way > but I'm not sure how I would check that. > > I can get around this by manually coercing each RangedData object to a > data.frame, but that approach seems suboptimal to me. > > Thanks, > > Jonathan > > -------- > > > a > RangedData with 3032 rows and 0 value columns across 25 spaces > space ranges | > <character> <iranges> | > 1 chr1 [1274369, 1274619] | > 2 chr1 [1310219, 1310569] | > 3 chr1 [1907419, 1907769] | > 4 chr1 [1983269, 1983469] | > 5 chr1 [2355219, 2355319] | > 6 chr1 [2431369, 2432219] | > 7 chr1 [2446219, 2446619] | > 8 chr1 [3441819, 3442169] | > 9 chr1 [3657769, 3657919] | > ... ... ... ... > 3024 chrX [106724271, 106724371] | > 3025 chrX [106983671, 106983771] | > 3026 chrX [108586171, 108586271] | > 3027 chrX [108781571, 108781671] | > 3028 chrX [110424871, 110425571] | > 3029 chrX [152256221, 152256371] | > 3030 chrX [152619071, 152619221] | > 3031 chrX [152661471, 152662221] | > 3032 chrX [152662571, 152662671] | > > > names(a) ##n.b. no ranges present for space "chrM" > [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" > "chr17" > [10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5" > [19] "chr6" "chr7" "chr8" "chr9" "chrM" "chrX" "chrY" > > > b > RangedData with 6486 rows and 0 value columns across 23 spaces > space ranges | > <character> <iranges> | > 1 chr1 [1274159, 1274912] | > 2 chr1 [1309807, 1310770] | > 3 chr1 [1532507, 1532754] | > 4 chr1 [1907180, 1907982] | > 5 chr1 [1983127, 1983848] | > 6 chr1 [2354988, 2355437] | > 7 chr1 [2431031, 2432299] | > 8 chr1 [2433599, 2433985] | > 9 chr1 [2446015, 2446750] | > ... ... ... ... > 6478 chrX [152618904, 152619429] | > 6479 chrX [152660747, 152661246] | > 6480 chrX [152661264, 152662298] | > 6481 chrX [152662420, 152662899] | > 6482 chrX [152664180, 152664467] | > 6483 chrX [152665288, 152665502] | > 6484 chrX [152758426, 152758742] | > 6485 chrX [153591715, 153591957] | > 6486 chrX [153849434, 153849749] | > > > names(b) ## (chrY, chrM not present in this object) > [1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" > "chr17" > [10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5" > [19] "chr6" "chr7" "chr8" "chr9" "chrX" > > > rbind(a,b) > Error in .Method(..., deparse.level = deparse.level) : > column names for arg 23 do not match those of first arg > > > traceback() > 17: stop("column names for arg ", i, " do not match those of first arg") > 16: .Method(..., deparse.level = deparse.level) > 15: eval(expr, envir, enclos) > 14: eval(.dotsCall, env) > 13: eval(.dotsCall, env) > 12: standardGeneric("rbind") > 11: function (..., deparse.level = 1) > standardGeneric("rbind")(<s4 object="" of="" class="" "dataframe"="">, <s4 object="" of=""> class "DataFrame">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">, <s4 object="" of="" class="" "dataframe"="">, > <s4 object="" of="" class="" "dataframe"="">) > 10: do.call(rbind, unname(x)) > 9: .compress.list(lapply(unlistData, as, elementTypeData)) > 8: newCompressedList("CompressedSplitDataFrameList", listData) > 7: SplitDataFrameList(do.call(Map, c(list(safe.rbind), dfs))) > 6: .Method(..., deparse.level = deparse.level) > 5: eval(expr, envir, enclos) > 4: eval(.dotsCall, env) > 3: eval(.dotsCall, env) > 2: standardGeneric("rbind") > 1: rbind(a, b) > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=en_GB.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.10.0 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.2 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0 > [4] GenomicRanges_1.2.1 tools_2.12.0 XML_3.2-0 > > > This communication is from Cancer Research UK. Our website is at > www.cancerresearchuk.org. We are a registered charity in England and Wales > (1089464) and in Scotland (SC041666) and a company limited by guarantee > registered in England and Wales under number 4325234. Our registered address > is Angel Building, 407 St John Street, London, EC1V 4AD. Our central > telephone number is 020 7242 0200. > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use of > the intended recipient(s). If you are not the intended recipient(s) please > note that any form of disclosure, distribution, copying or use of this > communication or the information in it or in any attachments is strictly > prohibited and may be unlawful. If you have received this communication in > error, please notify the sender and delete the email and destroy any copies > of it. > > E-mail communications cannot be guaranteed to be secure or error free, as > information could be intercepted, corrupted, amended, lost, destroyed, > arrive late or incomplete, or contain viruses. We do not accept liability > for any such matters or their consequences. Anyone who communicates with us > by e-mail is taken to accept the risks in doing so. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]