Odd behaviour with renameSeqlevels
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@alex-gutteridge-2935
Last seen 9.5 years ago
United States
Is this a bug in renameSeqlevels or expected behaviour? Note the weird ordering of chromosome names in txbygene (chrX between chr7 and chr8) which then results in misnaming when I try to use renameSeqlevels (everything after chr7 is off by one). The docs for renameSeqlevels aren't explicit in whether the renaming vector has to match the ordering of the original names, but I thought the point of making it named vector is that it doesn't? > library(TxDb.Hsapiens.UCSC.hg19.knownGene) Loading required package: GenomicFeatures Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: IRanges Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > txdb = TxDb.Hsapiens.UCSC.hg19.knownGene > txbygene = transcriptsBy(txdb,"gene") > tx = > renameSeqlevels(txbygene,c("chr1"="1","chr2"="2","chr3"="3","chr4"=" 4", + "chr5"="5","chr6"="6","chr7"="7","chr8"="8", + "chr9"="9","chr10"="10","chr11"="11","chr12"="12", + "chr13"="13","chr14"="14","chr15"="15","chr16"="16", + "chr17"="17","chr18"="18","chr19"="19","chr20"="20", + "chr21"="21","chr22"="22","chrX"="X")) > seqlevels(txbygene) [1] "chr1" "chr2" "chr3" [4] "chr4" "chr5" "chr6" [7] "chr7" "chrX" "chr8" [10] "chr9" "chr10" "chr11" [13] "chr12" "chr13" "chr14" [16] "chr15" "chr16" "chr17" [19] "chr18" "chr20" "chrY" [22] "chr19" "chr22" "chr21" [25] "chr6_ssto_hap7" "chr6_mcf_hap5" "chr6_cox_hap2" [28] "chr6_mann_hap4" "chr6_apd_hap1" "chr6_qbl_hap6" [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" "chr4_ctg9_hap1" [34] "chr1_gl000192_random" "chrUn_gl000225" "chr4_gl000194_random" [37] "chr4_gl000193_random" "chr9_gl000200_random" "chrUn_gl000222" [40] "chrUn_gl000212" "chr7_gl000195_random" "chrUn_gl000223" [43] "chrUn_gl000224" "chrUn_gl000219" "chr17_gl000205_random" [46] "chrUn_gl000215" "chrUn_gl000216" "chrUn_gl000217" [49] "chr9_gl000199_random" "chrUn_gl000211" "chrUn_gl000213" [52] "chrUn_gl000220" "chrUn_gl000218" "chr19_gl000209_random" [55] "chrUn_gl000221" "chrUn_gl000214" "chrUn_gl000228" [58] "chrUn_gl000227" "chr1_gl000191_random" "chr19_gl000208_random" [61] "chr9_gl000198_random" "chr17_gl000204_random" "chrUn_gl000233" [64] "chrUn_gl000237" "chrUn_gl000230" "chrUn_gl000242" [67] "chrUn_gl000243" "chrUn_gl000241" "chrUn_gl000236" [70] "chrUn_gl000240" "chr17_gl000206_random" "chrUn_gl000232" [73] "chrUn_gl000234" "chr11_gl000202_random" "chrUn_gl000238" [76] "chrUn_gl000244" "chrUn_gl000248" "chr8_gl000196_random" [79] "chrUn_gl000249" "chrUn_gl000246" "chr17_gl000203_random" [82] "chr8_gl000197_random" "chrUn_gl000245" "chrUn_gl000247" [85] "chr9_gl000201_random" "chrUn_gl000235" "chrUn_gl000239" [88] "chr21_gl000210_random" "chrUn_gl000231" "chrUn_gl000229" [91] "chrM" "chrUn_gl000226" "chr18_gl000207_random" > seqlevels(tx) [1] "1" "2" "3" [4] "4" "5" "6" [7] "7" "8" "9" [10] "10" "11" "12" [13] "13" "14" "15" [16] "16" "17" "18" [19] "19" "20" "chrY" [22] "21" "22" "X" [25] "chr6_ssto_hap7" "chr6_mcf_hap5" "chr6_cox_hap2" [28] "chr6_mann_hap4" "chr6_apd_hap1" "chr6_qbl_hap6" [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" "chr4_ctg9_hap1" [34] "chr1_gl000192_random" "chrUn_gl000225" "chr4_gl000194_random" [37] "chr4_gl000193_random" "chr9_gl000200_random" "chrUn_gl000222" [40] "chrUn_gl000212" "chr7_gl000195_random" "chrUn_gl000223" [43] "chrUn_gl000224" "chrUn_gl000219" "chr17_gl000205_random" [46] "chrUn_gl000215" "chrUn_gl000216" "chrUn_gl000217" [49] "chr9_gl000199_random" "chrUn_gl000211" "chrUn_gl000213" [52] "chrUn_gl000220" "chrUn_gl000218" "chr19_gl000209_random" [55] "chrUn_gl000221" "chrUn_gl000214" "chrUn_gl000228" [58] "chrUn_gl000227" "chr1_gl000191_random" "chr19_gl000208_random" [61] "chr9_gl000198_random" "chr17_gl000204_random" "chrUn_gl000233" [64] "chrUn_gl000237" "chrUn_gl000230" "chrUn_gl000242" [67] "chrUn_gl000243" "chrUn_gl000241" "chrUn_gl000236" [70] "chrUn_gl000240" "chr17_gl000206_random" "chrUn_gl000232" [73] "chrUn_gl000234" "chr11_gl000202_random" "chrUn_gl000238" [76] "chrUn_gl000244" "chrUn_gl000248" "chr8_gl000196_random" [79] "chrUn_gl000249" "chrUn_gl000246" "chr17_gl000203_random" [82] "chr8_gl000197_random" "chrUn_gl000245" "chrUn_gl000247" [85] "chr9_gl000201_random" "chrUn_gl000235" "chrUn_gl000239" [88] "chr21_gl000210_random" "chrUn_gl000231" "chrUn_gl000229" [91] "chrM" "chrUn_gl000226" "chr18_gl000207_random" > txbygene$'5327' GRanges with 6 ranges and 2 elementMetadata cols: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chr8 [42032236, 42050729] - | 31953 uc010lxf.1 [2] chr8 [42032236, 42050729] - | 31954 uc010lxg.1 [3] chr8 [42032236, 42065194] - | 31955 uc003xos.2 [4] chr8 [42032236, 42065194] - | 31956 uc003xot.2 [5] chr8 [42032236, 42065194] - | 31957 uc011lcm.1 [6] chr8 [42032236, 42065194] - | 31958 uc011lcn.1 --- seqlengths: chr1 chr2 ... chr18_gl000207_random 249250621 243199373 ... 4262 > tx$'5327' GRanges with 6 ranges and 2 elementMetadata cols: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] 9 [42032236, 42050729] - | 31953 uc010lxf.1 [2] 9 [42032236, 42050729] - | 31954 uc010lxg.1 [3] 9 [42032236, 42065194] - | 31955 uc003xos.2 [4] 9 [42032236, 42065194] - | 31956 uc003xot.2 [5] 9 [42032236, 42065194] - | 31957 uc011lcm.1 [6] 9 [42032236, 42065194] - | 31958 uc011lcn.1 --- seqlengths: 1 2 ... chr18_gl000207_random 249250621 243199373 ... 4262 > txbygene$'1956' GRanges with 11 ranges and 2 elementMetadata cols: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chr7 [55086725, 55224644] + | 28336 uc003tqh.3 [2] chr7 [55086725, 55236328] + | 28337 uc003tqi.3 [3] chr7 [55086725, 55238738] + | 28338 uc003tqj.3 [4] chr7 [55086725, 55270769] + | 28339 uc022adm.1 [5] chr7 [55086725, 55270769] + | 28340 uc010kzg.2 [6] chr7 [55086725, 55275031] + | 28341 uc003tqk.3 [7] chr7 [55086725, 55275031] + | 28342 uc022adn.1 [8] chr7 [55177540, 55275031] + | 28343 uc011kco.2 [9] chr7 [55224226, 55238906] + | 28345 uc011kcq.1 [10] chr7 [55224226, 55238906] + | 28346 uc011kcp.1 [11] chr7 [55248979, 55259567] + | 28349 uc022ado.1 --- seqlengths: chr1 chr2 ... chr18_gl000207_random 249250621 243199373 ... 4262 > tx$'1956' GRanges with 11 ranges and 2 elementMetadata cols: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] 7 [55086725, 55224644] + | 28336 uc003tqh.3 [2] 7 [55086725, 55236328] + | 28337 uc003tqi.3 [3] 7 [55086725, 55238738] + | 28338 uc003tqj.3 [4] 7 [55086725, 55270769] + | 28339 uc022adm.1 [5] 7 [55086725, 55270769] + | 28340 uc010kzg.2 [6] 7 [55086725, 55275031] + | 28341 uc003tqk.3 [7] 7 [55086725, 55275031] + | 28342 uc022adn.1 [8] 7 [55177540, 55275031] + | 28343 uc011kco.2 [9] 7 [55224226, 55238906] + | 28345 uc011kcq.1 [10] 7 [55224226, 55238906] + | 28346 uc011kcp.1 [11] 7 [55248979, 55259567] + | 28349 uc022ado.1 --- seqlengths: 1 2 ... chr18_gl000207_random 249250621 243199373 ... 4262> sessionInfo() R version 2.15.0 (2012-03-30) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 [2] GenomicFeatures_1.8.1 [3] AnnotationDbi_1.18.0 [4] Biobase_2.16.0 [5] GenomicRanges_1.8.3 [6] IRanges_1.14.2 [7] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] biomaRt_2.12.0 Biostrings_2.24.1 bitops_1.0-4.1 BSgenome_1.24.0 [5] DBI_0.2-5 RCurl_1.91-1 Rsamtools_1.8.3 RSQLite_0.11.1 [9] rtracklayer_1.16.1 stats4_2.15.0 tools_2.15.0 XML_3.9-4 [13] zlibbioc_1.2.0 -- Alex Gutteridge
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@valerie-obenchain-4275
Last seen 2.2 years ago
United States
Hi Alex, The ordering of the chromosome names displayed by seqlevels() comes from the seqlinfo object in the txdb. The ordering in the txdb or the txbygene before renaming is the same as after the renaming. txdb = TxDb.Hsapiens.UCSC.hg19.knownGene seqinfo(txdb) seqlevels(txdb) txbygene = transcriptsBy(txdb,"gene") seqinfo(txbygene) seqlevels(txbygene) This is not necessarily the same order as the seqnames (i.e., order of the ranges) in the txbygene object. seqnames(txbygene) Renaming the seqlevels has not changed the order of your txbygene ranges if that was the concern. No, the renaming vector does not need to match the ordering of the original names. Here is another way to prepare your new seqlevel names, nms <- seqlevels(txbygene)[1:24] vlu <- sub("chr", "", seqlevels(txbygene)[1:24], fixed=TRUE) names(vlu) <- nms renameSeqlevels(txbygene, vlu) Valerie On 05/02/2012 04:43 AM, Alex Gutteridge wrote: > Is this a bug in renameSeqlevels or expected behaviour? Note the weird > ordering of chromosome names in txbygene (chrX between chr7 and chr8) > which then results in misnaming when I try to use renameSeqlevels > (everything after chr7 is off by one). The docs for renameSeqlevels > aren't explicit in whether the renaming vector has to match the > ordering of the original names, but I thought the point of making it > named vector is that it doesn't? > >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) > Loading required package: GenomicFeatures > Loading required package: BiocGenerics > > Attaching package: ?BiocGenerics? > > The following object(s) are masked from ?package:stats?: > > xtabs > > The following object(s) are masked from ?package:base?: > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > get, intersect, lapply, Map, mapply, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, > rownames, sapply, setdiff, table, tapply, union, unique > > Loading required package: IRanges > Loading required package: GenomicRanges > Loading required package: AnnotationDbi > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene >> txbygene = transcriptsBy(txdb,"gene") >> tx = >> renameSeqlevels(txbygene,c("chr1"="1","chr2"="2","chr3"="3","chr4"= "4", > + > "chr5"="5","chr6"="6","chr7"="7","chr8"="8", > + > "chr9"="9","chr10"="10","chr11"="11","chr12"="12", > + > "chr13"="13","chr14"="14","chr15"="15","chr16"="16", > + > "chr17"="17","chr18"="18","chr19"="19","chr20"="20", > + "chr21"="21","chr22"="22","chrX"="X")) >> seqlevels(txbygene) > [1] "chr1" "chr2" "chr3" > [4] "chr4" "chr5" "chr6" > [7] "chr7" "chrX" "chr8" > [10] "chr9" "chr10" "chr11" > [13] "chr12" "chr13" "chr14" > [16] "chr15" "chr16" "chr17" > [19] "chr18" "chr20" "chrY" > [22] "chr19" "chr22" "chr21" > [25] "chr6_ssto_hap7" "chr6_mcf_hap5" "chr6_cox_hap2" > [28] "chr6_mann_hap4" "chr6_apd_hap1" "chr6_qbl_hap6" > [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" "chr4_ctg9_hap1" > [34] "chr1_gl000192_random" "chrUn_gl000225" > "chr4_gl000194_random" > [37] "chr4_gl000193_random" "chr9_gl000200_random" "chrUn_gl000222" > [40] "chrUn_gl000212" "chr7_gl000195_random" "chrUn_gl000223" > [43] "chrUn_gl000224" "chrUn_gl000219" > "chr17_gl000205_random" > [46] "chrUn_gl000215" "chrUn_gl000216" "chrUn_gl000217" > [49] "chr9_gl000199_random" "chrUn_gl000211" "chrUn_gl000213" > [52] "chrUn_gl000220" "chrUn_gl000218" > "chr19_gl000209_random" > [55] "chrUn_gl000221" "chrUn_gl000214" "chrUn_gl000228" > [58] "chrUn_gl000227" "chr1_gl000191_random" > "chr19_gl000208_random" > [61] "chr9_gl000198_random" "chr17_gl000204_random" "chrUn_gl000233" > [64] "chrUn_gl000237" "chrUn_gl000230" "chrUn_gl000242" > [67] "chrUn_gl000243" "chrUn_gl000241" "chrUn_gl000236" > [70] "chrUn_gl000240" "chr17_gl000206_random" "chrUn_gl000232" > [73] "chrUn_gl000234" "chr11_gl000202_random" "chrUn_gl000238" > [76] "chrUn_gl000244" "chrUn_gl000248" > "chr8_gl000196_random" > [79] "chrUn_gl000249" "chrUn_gl000246" > "chr17_gl000203_random" > [82] "chr8_gl000197_random" "chrUn_gl000245" "chrUn_gl000247" > [85] "chr9_gl000201_random" "chrUn_gl000235" "chrUn_gl000239" > [88] "chr21_gl000210_random" "chrUn_gl000231" "chrUn_gl000229" > [91] "chrM" "chrUn_gl000226" > "chr18_gl000207_random" >> seqlevels(tx) > [1] "1" "2" "3" > [4] "4" "5" "6" > [7] "7" "8" "9" > [10] "10" "11" "12" > [13] "13" "14" "15" > [16] "16" "17" "18" > [19] "19" "20" "chrY" > [22] "21" "22" "X" > [25] "chr6_ssto_hap7" "chr6_mcf_hap5" "chr6_cox_hap2" > [28] "chr6_mann_hap4" "chr6_apd_hap1" "chr6_qbl_hap6" > [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" "chr4_ctg9_hap1" > [34] "chr1_gl000192_random" "chrUn_gl000225" > "chr4_gl000194_random" > [37] "chr4_gl000193_random" "chr9_gl000200_random" "chrUn_gl000222" > [40] "chrUn_gl000212" "chr7_gl000195_random" "chrUn_gl000223" > [43] "chrUn_gl000224" "chrUn_gl000219" > "chr17_gl000205_random" > [46] "chrUn_gl000215" "chrUn_gl000216" "chrUn_gl000217" > [49] "chr9_gl000199_random" "chrUn_gl000211" "chrUn_gl000213" > [52] "chrUn_gl000220" "chrUn_gl000218" > "chr19_gl000209_random" > [55] "chrUn_gl000221" "chrUn_gl000214" "chrUn_gl000228" > [58] "chrUn_gl000227" "chr1_gl000191_random" > "chr19_gl000208_random" > [61] "chr9_gl000198_random" "chr17_gl000204_random" "chrUn_gl000233" > [64] "chrUn_gl000237" "chrUn_gl000230" "chrUn_gl000242" > [67] "chrUn_gl000243" "chrUn_gl000241" "chrUn_gl000236" > [70] "chrUn_gl000240" "chr17_gl000206_random" "chrUn_gl000232" > [73] "chrUn_gl000234" "chr11_gl000202_random" "chrUn_gl000238" > [76] "chrUn_gl000244" "chrUn_gl000248" > "chr8_gl000196_random" > [79] "chrUn_gl000249" "chrUn_gl000246" > "chr17_gl000203_random" > [82] "chr8_gl000197_random" "chrUn_gl000245" "chrUn_gl000247" > [85] "chr9_gl000201_random" "chrUn_gl000235" "chrUn_gl000239" > [88] "chr21_gl000210_random" "chrUn_gl000231" "chrUn_gl000229" > [91] "chrM" "chrUn_gl000226" > "chr18_gl000207_random" >> txbygene$'5327' > GRanges with 6 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] chr8 [42032236, 42050729] - | 31953 uc010lxf.1 > [2] chr8 [42032236, 42050729] - | 31954 uc010lxg.1 > [3] chr8 [42032236, 42065194] - | 31955 uc003xos.2 > [4] chr8 [42032236, 42065194] - | 31956 uc003xot.2 > [5] chr8 [42032236, 42065194] - | 31957 uc011lcm.1 > [6] chr8 [42032236, 42065194] - | 31958 uc011lcn.1 > --- > seqlengths: > chr1 chr2 ... chr18_gl000207_random > 249250621 243199373 ... 4262 >> tx$'5327' > GRanges with 6 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] 9 [42032236, 42050729] - | 31953 uc010lxf.1 > [2] 9 [42032236, 42050729] - | 31954 uc010lxg.1 > [3] 9 [42032236, 42065194] - | 31955 uc003xos.2 > [4] 9 [42032236, 42065194] - | 31956 uc003xot.2 > [5] 9 [42032236, 42065194] - | 31957 uc011lcm.1 > [6] 9 [42032236, 42065194] - | 31958 uc011lcn.1 > --- > seqlengths: > 1 2 ... chr18_gl000207_random > 249250621 243199373 ... 4262 >> txbygene$'1956' > GRanges with 11 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] chr7 [55086725, 55224644] + | 28336 uc003tqh.3 > [2] chr7 [55086725, 55236328] + | 28337 uc003tqi.3 > [3] chr7 [55086725, 55238738] + | 28338 uc003tqj.3 > [4] chr7 [55086725, 55270769] + | 28339 uc022adm.1 > [5] chr7 [55086725, 55270769] + | 28340 uc010kzg.2 > [6] chr7 [55086725, 55275031] + | 28341 uc003tqk.3 > [7] chr7 [55086725, 55275031] + | 28342 uc022adn.1 > [8] chr7 [55177540, 55275031] + | 28343 uc011kco.2 > [9] chr7 [55224226, 55238906] + | 28345 uc011kcq.1 > [10] chr7 [55224226, 55238906] + | 28346 uc011kcp.1 > [11] chr7 [55248979, 55259567] + | 28349 uc022ado.1 > --- > seqlengths: > chr1 chr2 ... chr18_gl000207_random > 249250621 243199373 ... 4262 >> tx$'1956' > GRanges with 11 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] 7 [55086725, 55224644] + | 28336 uc003tqh.3 > [2] 7 [55086725, 55236328] + | 28337 uc003tqi.3 > [3] 7 [55086725, 55238738] + | 28338 uc003tqj.3 > [4] 7 [55086725, 55270769] + | 28339 uc022adm.1 > [5] 7 [55086725, 55270769] + | 28340 uc010kzg.2 > [6] 7 [55086725, 55275031] + | 28341 uc003tqk.3 > [7] 7 [55086725, 55275031] + | 28342 uc022adn.1 > [8] 7 [55177540, 55275031] + | 28343 uc011kco.2 > [9] 7 [55224226, 55238906] + | 28345 uc011kcq.1 > [10] 7 [55224226, 55238906] + | 28346 uc011kcp.1 > [11] 7 [55248979, 55259567] + | 28349 uc022ado.1 > --- > seqlengths: > 1 2 ... chr18_gl000207_random > 249250621 243199373 ... > 4262> sessionInfo() > R version 2.15.0 (2012-03-30) > 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 > [2] GenomicFeatures_1.8.1 > [3] AnnotationDbi_1.18.0 > [4] Biobase_2.16.0 > [5] GenomicRanges_1.8.3 > [6] IRanges_1.14.2 > [7] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.12.0 Biostrings_2.24.1 bitops_1.0-4.1 > BSgenome_1.24.0 > [5] DBI_0.2-5 RCurl_1.91-1 Rsamtools_1.8.3 > RSQLite_0.11.1 > [9] rtracklayer_1.16.1 stats4_2.15.0 tools_2.15.0 XML_3.9-4 > [13] zlibbioc_1.2.0 >
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I'm sorry Alex, I missed your point the first time. Yes, there was a bug in renameSeqlevels() wrt changing the chromosome names when the renaming vector was out of order with 'x'. Now fixed in 1.8.5 release /1.9.13 devel. Thanks for reporting this. Valerie On 05/02/2012 09:25 AM, Valerie Obenchain wrote: > Hi Alex, > > The ordering of the chromosome names displayed by seqlevels() comes > from the seqlinfo object in the txdb. The ordering in the txdb or the > txbygene before renaming is the same as after the renaming. > > txdb = TxDb.Hsapiens.UCSC.hg19.knownGene > seqinfo(txdb) > seqlevels(txdb) > > txbygene = transcriptsBy(txdb,"gene") > seqinfo(txbygene) > seqlevels(txbygene) > > This is not necessarily the same order as the seqnames (i.e., order of > the ranges) in the txbygene object. > seqnames(txbygene) > > Renaming the seqlevels has not changed the order of your txbygene > ranges if that was the concern. No, the renaming vector does not need > to match the ordering of the original names. > > Here is another way to prepare your new seqlevel names, > > nms <- seqlevels(txbygene)[1:24] > vlu <- sub("chr", "", seqlevels(txbygene)[1:24], fixed=TRUE) > names(vlu) <- nms > renameSeqlevels(txbygene, vlu) > > Valerie > > > On 05/02/2012 04:43 AM, Alex Gutteridge wrote: >> Is this a bug in renameSeqlevels or expected behaviour? Note the >> weird ordering of chromosome names in txbygene (chrX between chr7 and >> chr8) which then results in misnaming when I try to use >> renameSeqlevels (everything after chr7 is off by one). The docs for >> renameSeqlevels aren't explicit in whether the renaming vector has to >> match the ordering of the original names, but I thought the point of >> making it named vector is that it doesn't? >> >>> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> Loading required package: GenomicFeatures >> Loading required package: BiocGenerics >> >> Attaching package: ?BiocGenerics? >> >> The following object(s) are masked from ?package:stats?: >> >> xtabs >> >> The following object(s) are masked from ?package:base?: >> >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, >> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, >> pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, >> rownames, sapply, setdiff, table, tapply, union, unique >> >> Loading required package: IRanges >> Loading required package: GenomicRanges >> Loading required package: AnnotationDbi >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >>> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene >>> txbygene = transcriptsBy(txdb,"gene") >>> tx = >>> renameSeqlevels(txbygene,c("chr1"="1","chr2"="2","chr3"="3","chr4" ="4", >> + >> "chr5"="5","chr6"="6","chr7"="7","chr8"="8", >> + >> "chr9"="9","chr10"="10","chr11"="11","chr12"="12", >> + >> "chr13"="13","chr14"="14","chr15"="15","chr16"="16", >> + >> "chr17"="17","chr18"="18","chr19"="19","chr20"="20", >> + "chr21"="21","chr22"="22","chrX"="X")) >>> seqlevels(txbygene) >> [1] "chr1" "chr2" "chr3" >> [4] "chr4" "chr5" "chr6" >> [7] "chr7" "chrX" "chr8" >> [10] "chr9" "chr10" "chr11" >> [13] "chr12" "chr13" "chr14" >> [16] "chr15" "chr16" "chr17" >> [19] "chr18" "chr20" "chrY" >> [22] "chr19" "chr22" "chr21" >> [25] "chr6_ssto_hap7" "chr6_mcf_hap5" "chr6_cox_hap2" >> [28] "chr6_mann_hap4" "chr6_apd_hap1" "chr6_qbl_hap6" >> [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" "chr4_ctg9_hap1" >> [34] "chr1_gl000192_random" "chrUn_gl000225" >> "chr4_gl000194_random" >> [37] "chr4_gl000193_random" "chr9_gl000200_random" "chrUn_gl000222" >> [40] "chrUn_gl000212" "chr7_gl000195_random" "chrUn_gl000223" >> [43] "chrUn_gl000224" "chrUn_gl000219" >> "chr17_gl000205_random" >> [46] "chrUn_gl000215" "chrUn_gl000216" "chrUn_gl000217" >> [49] "chr9_gl000199_random" "chrUn_gl000211" "chrUn_gl000213" >> [52] "chrUn_gl000220" "chrUn_gl000218" >> "chr19_gl000209_random" >> [55] "chrUn_gl000221" "chrUn_gl000214" "chrUn_gl000228" >> [58] "chrUn_gl000227" "chr1_gl000191_random" >> "chr19_gl000208_random" >> [61] "chr9_gl000198_random" "chr17_gl000204_random" "chrUn_gl000233" >> [64] "chrUn_gl000237" "chrUn_gl000230" "chrUn_gl000242" >> [67] "chrUn_gl000243" "chrUn_gl000241" "chrUn_gl000236" >> [70] "chrUn_gl000240" "chr17_gl000206_random" "chrUn_gl000232" >> [73] "chrUn_gl000234" "chr11_gl000202_random" "chrUn_gl000238" >> [76] "chrUn_gl000244" "chrUn_gl000248" >> "chr8_gl000196_random" >> [79] "chrUn_gl000249" "chrUn_gl000246" >> "chr17_gl000203_random" >> [82] "chr8_gl000197_random" "chrUn_gl000245" "chrUn_gl000247" >> [85] "chr9_gl000201_random" "chrUn_gl000235" "chrUn_gl000239" >> [88] "chr21_gl000210_random" "chrUn_gl000231" "chrUn_gl000229" >> [91] "chrM" "chrUn_gl000226" >> "chr18_gl000207_random" >>> seqlevels(tx) >> [1] "1" "2" "3" >> [4] "4" "5" "6" >> [7] "7" "8" "9" >> [10] "10" "11" "12" >> [13] "13" "14" "15" >> [16] "16" "17" "18" >> [19] "19" "20" "chrY" >> [22] "21" "22" "X" >> [25] "chr6_ssto_hap7" "chr6_mcf_hap5" "chr6_cox_hap2" >> [28] "chr6_mann_hap4" "chr6_apd_hap1" "chr6_qbl_hap6" >> [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" "chr4_ctg9_hap1" >> [34] "chr1_gl000192_random" "chrUn_gl000225" >> "chr4_gl000194_random" >> [37] "chr4_gl000193_random" "chr9_gl000200_random" "chrUn_gl000222" >> [40] "chrUn_gl000212" "chr7_gl000195_random" "chrUn_gl000223" >> [43] "chrUn_gl000224" "chrUn_gl000219" >> "chr17_gl000205_random" >> [46] "chrUn_gl000215" "chrUn_gl000216" "chrUn_gl000217" >> [49] "chr9_gl000199_random" "chrUn_gl000211" "chrUn_gl000213" >> [52] "chrUn_gl000220" "chrUn_gl000218" >> "chr19_gl000209_random" >> [55] "chrUn_gl000221" "chrUn_gl000214" "chrUn_gl000228" >> [58] "chrUn_gl000227" "chr1_gl000191_random" >> "chr19_gl000208_random" >> [61] "chr9_gl000198_random" "chr17_gl000204_random" "chrUn_gl000233" >> [64] "chrUn_gl000237" "chrUn_gl000230" "chrUn_gl000242" >> [67] "chrUn_gl000243" "chrUn_gl000241" "chrUn_gl000236" >> [70] "chrUn_gl000240" "chr17_gl000206_random" "chrUn_gl000232" >> [73] "chrUn_gl000234" "chr11_gl000202_random" "chrUn_gl000238" >> [76] "chrUn_gl000244" "chrUn_gl000248" >> "chr8_gl000196_random" >> [79] "chrUn_gl000249" "chrUn_gl000246" >> "chr17_gl000203_random" >> [82] "chr8_gl000197_random" "chrUn_gl000245" "chrUn_gl000247" >> [85] "chr9_gl000201_random" "chrUn_gl000235" "chrUn_gl000239" >> [88] "chr21_gl000210_random" "chrUn_gl000231" "chrUn_gl000229" >> [91] "chrM" "chrUn_gl000226" >> "chr18_gl000207_random" >>> txbygene$'5327' >> GRanges with 6 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> | <integer> <character> >> [1] chr8 [42032236, 42050729] - | 31953 uc010lxf.1 >> [2] chr8 [42032236, 42050729] - | 31954 uc010lxg.1 >> [3] chr8 [42032236, 42065194] - | 31955 uc003xos.2 >> [4] chr8 [42032236, 42065194] - | 31956 uc003xot.2 >> [5] chr8 [42032236, 42065194] - | 31957 uc011lcm.1 >> [6] chr8 [42032236, 42065194] - | 31958 uc011lcn.1 >> --- >> seqlengths: >> chr1 chr2 ... chr18_gl000207_random >> 249250621 243199373 ... 4262 >>> tx$'5327' >> GRanges with 6 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> | <integer> <character> >> [1] 9 [42032236, 42050729] - | 31953 uc010lxf.1 >> [2] 9 [42032236, 42050729] - | 31954 uc010lxg.1 >> [3] 9 [42032236, 42065194] - | 31955 uc003xos.2 >> [4] 9 [42032236, 42065194] - | 31956 uc003xot.2 >> [5] 9 [42032236, 42065194] - | 31957 uc011lcm.1 >> [6] 9 [42032236, 42065194] - | 31958 uc011lcn.1 >> --- >> seqlengths: >> 1 2 ... chr18_gl000207_random >> 249250621 243199373 ... 4262 >>> txbygene$'1956' >> GRanges with 11 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> | <integer> <character> >> [1] chr7 [55086725, 55224644] + | 28336 uc003tqh.3 >> [2] chr7 [55086725, 55236328] + | 28337 uc003tqi.3 >> [3] chr7 [55086725, 55238738] + | 28338 uc003tqj.3 >> [4] chr7 [55086725, 55270769] + | 28339 uc022adm.1 >> [5] chr7 [55086725, 55270769] + | 28340 uc010kzg.2 >> [6] chr7 [55086725, 55275031] + | 28341 uc003tqk.3 >> [7] chr7 [55086725, 55275031] + | 28342 uc022adn.1 >> [8] chr7 [55177540, 55275031] + | 28343 uc011kco.2 >> [9] chr7 [55224226, 55238906] + | 28345 uc011kcq.1 >> [10] chr7 [55224226, 55238906] + | 28346 uc011kcp.1 >> [11] chr7 [55248979, 55259567] + | 28349 uc022ado.1 >> --- >> seqlengths: >> chr1 chr2 ... chr18_gl000207_random >> 249250621 243199373 ... 4262 >>> tx$'1956' >> GRanges with 11 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> | <integer> <character> >> [1] 7 [55086725, 55224644] + | 28336 uc003tqh.3 >> [2] 7 [55086725, 55236328] + | 28337 uc003tqi.3 >> [3] 7 [55086725, 55238738] + | 28338 uc003tqj.3 >> [4] 7 [55086725, 55270769] + | 28339 uc022adm.1 >> [5] 7 [55086725, 55270769] + | 28340 uc010kzg.2 >> [6] 7 [55086725, 55275031] + | 28341 uc003tqk.3 >> [7] 7 [55086725, 55275031] + | 28342 uc022adn.1 >> [8] 7 [55177540, 55275031] + | 28343 uc011kco.2 >> [9] 7 [55224226, 55238906] + | 28345 uc011kcq.1 >> [10] 7 [55224226, 55238906] + | 28346 uc011kcp.1 >> [11] 7 [55248979, 55259567] + | 28349 uc022ado.1 >> --- >> seqlengths: >> 1 2 ... chr18_gl000207_random >> 249250621 243199373 ... >> 4262> sessionInfo() >> R version 2.15.0 (2012-03-30) >> 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C 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] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 >> [2] GenomicFeatures_1.8.1 >> [3] AnnotationDbi_1.18.0 >> [4] Biobase_2.16.0 >> [5] GenomicRanges_1.8.3 >> [6] IRanges_1.14.2 >> [7] BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.12.0 Biostrings_2.24.1 bitops_1.0-4.1 >> BSgenome_1.24.0 >> [5] DBI_0.2-5 RCurl_1.91-1 Rsamtools_1.8.3 >> RSQLite_0.11.1 >> [9] rtracklayer_1.16.1 stats4_2.15.0 tools_2.15.0 XML_3.9-4 >> [13] zlibbioc_1.2.0 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Entering edit mode
Thanks Valerie. On 02.05.2012 17:46, Valerie Obenchain wrote: > I'm sorry Alex, I missed your point the first time. Yes, there was a > bug in renameSeqlevels() wrt changing the chromosome names when the > renaming vector was out of order with 'x'. > > Now fixed in 1.8.5 release /1.9.13 devel. Thanks for reporting this. > > Valerie > > > > On 05/02/2012 09:25 AM, Valerie Obenchain wrote: >> Hi Alex, >> >> The ordering of the chromosome names displayed by seqlevels() comes >> from the seqlinfo object in the txdb. The ordering in the txdb or the >> txbygene before renaming is the same as after the renaming. >> >> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene >> seqinfo(txdb) >> seqlevels(txdb) >> >> txbygene = transcriptsBy(txdb,"gene") >> seqinfo(txbygene) >> seqlevels(txbygene) >> >> This is not necessarily the same order as the seqnames (i.e., order >> of the ranges) in the txbygene object. >> seqnames(txbygene) >> >> Renaming the seqlevels has not changed the order of your txbygene >> ranges if that was the concern. No, the renaming vector does not need >> to match the ordering of the original names. >> >> Here is another way to prepare your new seqlevel names, >> >> nms <- seqlevels(txbygene)[1:24] >> vlu <- sub("chr", "", seqlevels(txbygene)[1:24], fixed=TRUE) >> names(vlu) <- nms >> renameSeqlevels(txbygene, vlu) >> >> Valerie >> >> >> On 05/02/2012 04:43 AM, Alex Gutteridge wrote: >>> Is this a bug in renameSeqlevels or expected behaviour? Note the >>> weird ordering of chromosome names in txbygene (chrX between chr7 and >>> chr8) which then results in misnaming when I try to use >>> renameSeqlevels (everything after chr7 is off by one). The docs for >>> renameSeqlevels aren't explicit in whether the renaming vector has to >>> match the ordering of the original names, but I thought the point of >>> making it named vector is that it doesn't? >>> >>>> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >>> Loading required package: GenomicFeatures >>> Loading required package: BiocGenerics >>> >>> Attaching package: ?BiocGenerics? >>> >>> The following object(s) are masked from ?package:stats?: >>> >>> xtabs >>> >>> The following object(s) are masked from ?package:base?: >>> >>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, >>> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, >>> pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, >>> rownames, sapply, setdiff, table, tapply, union, unique >>> >>> Loading required package: IRanges >>> Loading required package: GenomicRanges >>> Loading required package: AnnotationDbi >>> Loading required package: Biobase >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material; view with >>> 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>> >>>> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene >>>> txbygene = transcriptsBy(txdb,"gene") >>>> tx = >>>> renameSeqlevels(txbygene,c("chr1"="1","chr2"="2","chr3"="3","chr4 "="4", >>> + >>> "chr5"="5","chr6"="6","chr7"="7","chr8"="8", >>> + >>> "chr9"="9","chr10"="10","chr11"="11","chr12"="12", >>> + >>> "chr13"="13","chr14"="14","chr15"="15","chr16"="16", >>> + >>> "chr17"="17","chr18"="18","chr19"="19","chr20"="20", >>> + >>> "chr21"="21","chr22"="22","chrX"="X")) >>>> seqlevels(txbygene) >>> [1] "chr1" "chr2" "chr3" >>> [4] "chr4" "chr5" "chr6" >>> [7] "chr7" "chrX" "chr8" >>> [10] "chr9" "chr10" "chr11" >>> [13] "chr12" "chr13" "chr14" >>> [16] "chr15" "chr16" "chr17" >>> [19] "chr18" "chr20" "chrY" >>> [22] "chr19" "chr22" "chr21" >>> [25] "chr6_ssto_hap7" "chr6_mcf_hap5" >>> "chr6_cox_hap2" >>> [28] "chr6_mann_hap4" "chr6_apd_hap1" >>> "chr6_qbl_hap6" >>> [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" >>> "chr4_ctg9_hap1" >>> [34] "chr1_gl000192_random" "chrUn_gl000225" >>> "chr4_gl000194_random" >>> [37] "chr4_gl000193_random" "chr9_gl000200_random" >>> "chrUn_gl000222" >>> [40] "chrUn_gl000212" "chr7_gl000195_random" >>> "chrUn_gl000223" >>> [43] "chrUn_gl000224" "chrUn_gl000219" >>> "chr17_gl000205_random" >>> [46] "chrUn_gl000215" "chrUn_gl000216" >>> "chrUn_gl000217" >>> [49] "chr9_gl000199_random" "chrUn_gl000211" >>> "chrUn_gl000213" >>> [52] "chrUn_gl000220" "chrUn_gl000218" >>> "chr19_gl000209_random" >>> [55] "chrUn_gl000221" "chrUn_gl000214" >>> "chrUn_gl000228" >>> [58] "chrUn_gl000227" "chr1_gl000191_random" >>> "chr19_gl000208_random" >>> [61] "chr9_gl000198_random" "chr17_gl000204_random" >>> "chrUn_gl000233" >>> [64] "chrUn_gl000237" "chrUn_gl000230" >>> "chrUn_gl000242" >>> [67] "chrUn_gl000243" "chrUn_gl000241" >>> "chrUn_gl000236" >>> [70] "chrUn_gl000240" "chr17_gl000206_random" >>> "chrUn_gl000232" >>> [73] "chrUn_gl000234" "chr11_gl000202_random" >>> "chrUn_gl000238" >>> [76] "chrUn_gl000244" "chrUn_gl000248" >>> "chr8_gl000196_random" >>> [79] "chrUn_gl000249" "chrUn_gl000246" >>> "chr17_gl000203_random" >>> [82] "chr8_gl000197_random" "chrUn_gl000245" >>> "chrUn_gl000247" >>> [85] "chr9_gl000201_random" "chrUn_gl000235" >>> "chrUn_gl000239" >>> [88] "chr21_gl000210_random" "chrUn_gl000231" >>> "chrUn_gl000229" >>> [91] "chrM" "chrUn_gl000226" >>> "chr18_gl000207_random" >>>> seqlevels(tx) >>> [1] "1" "2" "3" >>> [4] "4" "5" "6" >>> [7] "7" "8" "9" >>> [10] "10" "11" "12" >>> [13] "13" "14" "15" >>> [16] "16" "17" "18" >>> [19] "19" "20" "chrY" >>> [22] "21" "22" "X" >>> [25] "chr6_ssto_hap7" "chr6_mcf_hap5" >>> "chr6_cox_hap2" >>> [28] "chr6_mann_hap4" "chr6_apd_hap1" >>> "chr6_qbl_hap6" >>> [31] "chr6_dbb_hap3" "chr17_ctg5_hap1" >>> "chr4_ctg9_hap1" >>> [34] "chr1_gl000192_random" "chrUn_gl000225" >>> "chr4_gl000194_random" >>> [37] "chr4_gl000193_random" "chr9_gl000200_random" >>> "chrUn_gl000222" >>> [40] "chrUn_gl000212" "chr7_gl000195_random" >>> "chrUn_gl000223" >>> [43] "chrUn_gl000224" "chrUn_gl000219" >>> "chr17_gl000205_random" >>> [46] "chrUn_gl000215" "chrUn_gl000216" >>> "chrUn_gl000217" >>> [49] "chr9_gl000199_random" "chrUn_gl000211" >>> "chrUn_gl000213" >>> [52] "chrUn_gl000220" "chrUn_gl000218" >>> "chr19_gl000209_random" >>> [55] "chrUn_gl000221" "chrUn_gl000214" >>> "chrUn_gl000228" >>> [58] "chrUn_gl000227" "chr1_gl000191_random" >>> "chr19_gl000208_random" >>> [61] "chr9_gl000198_random" "chr17_gl000204_random" >>> "chrUn_gl000233" >>> [64] "chrUn_gl000237" "chrUn_gl000230" >>> "chrUn_gl000242" >>> [67] "chrUn_gl000243" "chrUn_gl000241" >>> "chrUn_gl000236" >>> [70] "chrUn_gl000240" "chr17_gl000206_random" >>> "chrUn_gl000232" >>> [73] "chrUn_gl000234" "chr11_gl000202_random" >>> "chrUn_gl000238" >>> [76] "chrUn_gl000244" "chrUn_gl000248" >>> "chr8_gl000196_random" >>> [79] "chrUn_gl000249" "chrUn_gl000246" >>> "chr17_gl000203_random" >>> [82] "chr8_gl000197_random" "chrUn_gl000245" >>> "chrUn_gl000247" >>> [85] "chr9_gl000201_random" "chrUn_gl000235" >>> "chrUn_gl000239" >>> [88] "chr21_gl000210_random" "chrUn_gl000231" >>> "chrUn_gl000229" >>> [91] "chrM" "chrUn_gl000226" >>> "chr18_gl000207_random" >>>> txbygene$'5327' >>> GRanges with 6 ranges and 2 elementMetadata cols: >>> seqnames ranges strand | tx_id tx_name >>> <rle> <iranges> <rle> | <integer> <character> >>> [1] chr8 [42032236, 42050729] - | 31953 uc010lxf.1 >>> [2] chr8 [42032236, 42050729] - | 31954 uc010lxg.1 >>> [3] chr8 [42032236, 42065194] - | 31955 uc003xos.2 >>> [4] chr8 [42032236, 42065194] - | 31956 uc003xot.2 >>> [5] chr8 [42032236, 42065194] - | 31957 uc011lcm.1 >>> [6] chr8 [42032236, 42065194] - | 31958 uc011lcn.1 >>> --- >>> seqlengths: >>> chr1 chr2 ... >>> chr18_gl000207_random >>> 249250621 243199373 ... >>> 4262 >>>> tx$'5327' >>> GRanges with 6 ranges and 2 elementMetadata cols: >>> seqnames ranges strand | tx_id tx_name >>> <rle> <iranges> <rle> | <integer> <character> >>> [1] 9 [42032236, 42050729] - | 31953 uc010lxf.1 >>> [2] 9 [42032236, 42050729] - | 31954 uc010lxg.1 >>> [3] 9 [42032236, 42065194] - | 31955 uc003xos.2 >>> [4] 9 [42032236, 42065194] - | 31956 uc003xot.2 >>> [5] 9 [42032236, 42065194] - | 31957 uc011lcm.1 >>> [6] 9 [42032236, 42065194] - | 31958 uc011lcn.1 >>> --- >>> seqlengths: >>> 1 2 ... >>> chr18_gl000207_random >>> 249250621 243199373 ... >>> 4262 >>>> txbygene$'1956' >>> GRanges with 11 ranges and 2 elementMetadata cols: >>> seqnames ranges strand | tx_id tx_name >>> <rle> <iranges> <rle> | <integer> <character> >>> [1] chr7 [55086725, 55224644] + | 28336 uc003tqh.3 >>> [2] chr7 [55086725, 55236328] + | 28337 uc003tqi.3 >>> [3] chr7 [55086725, 55238738] + | 28338 uc003tqj.3 >>> [4] chr7 [55086725, 55270769] + | 28339 uc022adm.1 >>> [5] chr7 [55086725, 55270769] + | 28340 uc010kzg.2 >>> [6] chr7 [55086725, 55275031] + | 28341 uc003tqk.3 >>> [7] chr7 [55086725, 55275031] + | 28342 uc022adn.1 >>> [8] chr7 [55177540, 55275031] + | 28343 uc011kco.2 >>> [9] chr7 [55224226, 55238906] + | 28345 uc011kcq.1 >>> [10] chr7 [55224226, 55238906] + | 28346 uc011kcp.1 >>> [11] chr7 [55248979, 55259567] + | 28349 uc022ado.1 >>> --- >>> seqlengths: >>> chr1 chr2 ... >>> chr18_gl000207_random >>> 249250621 243199373 ... >>> 4262 >>>> tx$'1956' >>> GRanges with 11 ranges and 2 elementMetadata cols: >>> seqnames ranges strand | tx_id tx_name >>> <rle> <iranges> <rle> | <integer> <character> >>> [1] 7 [55086725, 55224644] + | 28336 uc003tqh.3 >>> [2] 7 [55086725, 55236328] + | 28337 uc003tqi.3 >>> [3] 7 [55086725, 55238738] + | 28338 uc003tqj.3 >>> [4] 7 [55086725, 55270769] + | 28339 uc022adm.1 >>> [5] 7 [55086725, 55270769] + | 28340 uc010kzg.2 >>> [6] 7 [55086725, 55275031] + | 28341 uc003tqk.3 >>> [7] 7 [55086725, 55275031] + | 28342 uc022adn.1 >>> [8] 7 [55177540, 55275031] + | 28343 uc011kco.2 >>> [9] 7 [55224226, 55238906] + | 28345 uc011kcq.1 >>> [10] 7 [55224226, 55238906] + | 28346 uc011kcp.1 >>> [11] 7 [55248979, 55259567] + | 28349 uc022ado.1 >>> --- >>> seqlengths: >>> 1 2 ... >>> chr18_gl000207_random >>> 249250621 243199373 ... >>> 4262> sessionInfo() >>> R version 2.15.0 (2012-03-30) >>> 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C 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] TxDb.Hsapiens.UCSC.hg19.knownGene_2.7.1 >>> [2] GenomicFeatures_1.8.1 >>> [3] AnnotationDbi_1.18.0 >>> [4] Biobase_2.16.0 >>> [5] GenomicRanges_1.8.3 >>> [6] IRanges_1.14.2 >>> [7] BiocGenerics_0.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] biomaRt_2.12.0 Biostrings_2.24.1 bitops_1.0-4.1 >>> BSgenome_1.24.0 >>> [5] DBI_0.2-5 RCurl_1.91-1 Rsamtools_1.8.3 >>> RSQLite_0.11.1 >>> [9] rtracklayer_1.16.1 stats4_2.15.0 tools_2.15.0 >>> XML_3.9-4 >>> [13] zlibbioc_1.2.0 >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor -- Alex Gutteridge
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