Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Support for other than Ensembl seqlevel styleDescriptionThe methods and functions on this help page allow to integrate
Usage## S4 method for signature 'EnsDb' seqlevelsStyle(x) ## S4 replacement method for signature 'EnsDb' seqlevelsStyle(x) <- value ## S4 method for signature 'EnsDb' supportedSeqlevelsStyles(x) Arguments(In alphabetic order)
ValueFor For Methods and Functions
NoteThe mapping between different seqname styles is performed based on
data provided by the Author(s)Johannes Rainer See Also
Examples
library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75
## Get the internal, default seqlevel style.
seqlevelsStyle(edb)
## Get the seqlevels from the database.
seqlevels(edb)
## Get all supported mappings for the organism of the EnsDb.
supportedSeqlevelsStyles(edb)
## Change the seqlevels to UCSC style.
seqlevelsStyle(edb) <- "UCSC"
seqlevels(edb)
## Change the option ensembldb.seqnameNotFound to return NA in case
## the seqname can not be mapped form Ensembl to UCSC.
options(ensembldb.seqnameNotFound=NA)
seqlevels(edb)
## Restoring the original setting.
options(ensembldb.seqnameNotFound="ORIGINAL")
## Integrate Ensembl based annotations with a BSgenome package that is based on
## UCSC style seqnames.
library(BSgenome.Hsapiens.UCSC.hg19)
bsg <- BSgenome.Hsapiens.UCSC.hg19
## Get the genome version
unique(genome(bsg))
unique(genome(edb))
## Although differently named, both represent genome build GRCh37.
## Extract the full transcript sequences of all lincRNAs encoded on chromsome Y.
yTxSeqs <- extractTranscriptSeqs(bsg, exonsBy(edb, "tx",
filter=list(SeqnameFilter("chrY"),
GenebiotypeFilter("lincRNA"))))
yTxSeqs
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(ensembldb)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
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")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ensembldb/EnsDb-seqlevels.Rd_%03d_medium.png", width=480, height=480)
> ### Name: seqlevelsStyle
> ### Title: Support for other than Ensembl seqlevel style
> ### Aliases: seqlevelsStyle seqlevelsStyle,EnsDb-method seqlevelsStyle<-
> ### seqlevelsStyle<-,EnsDb-method supportedSeqlevelsStyles
> ### supportedSeqlevelsStyles,EnsDb-method
> ### Keywords: classes
>
> ### ** Examples
>
>
> library(EnsDb.Hsapiens.v75)
> edb <- EnsDb.Hsapiens.v75
>
> ## Get the internal, default seqlevel style.
> seqlevelsStyle(edb)
[1] "Ensembl"
>
> ## Get the seqlevels from the database.
> seqlevels(edb)
[1] "1" "10"
[3] "11" "12"
[5] "13" "14"
[7] "15" "16"
[9] "17" "18"
[11] "19" "2"
[13] "20" "21"
[15] "22" "3"
[17] "4" "5"
[19] "6" "7"
[21] "8" "9"
[23] "GL000191.1" "GL000192.1"
[25] "GL000193.1" "GL000194.1"
[27] "GL000195.1" "GL000196.1"
[29] "GL000199.1" "GL000201.1"
[31] "GL000204.1" "GL000205.1"
[33] "GL000209.1" "GL000211.1"
[35] "GL000212.1" "GL000213.1"
[37] "GL000215.1" "GL000216.1"
[39] "GL000218.1" "GL000219.1"
[41] "GL000220.1" "GL000221.1"
[43] "GL000222.1" "GL000223.1"
[45] "GL000224.1" "GL000225.1"
[47] "GL000228.1" "GL000229.1"
[49] "GL000230.1" "GL000231.1"
[51] "GL000233.1" "GL000236.1"
[53] "GL000237.1" "GL000240.1"
[55] "GL000241.1" "GL000242.1"
[57] "GL000243.1" "GL000247.1"
[59] "HG1007_PATCH" "HG1032_PATCH"
[61] "HG104_HG975_PATCH" "HG1063_PATCH"
[63] "HG1074_PATCH" "HG1079_PATCH"
[65] "HG1082_HG167_PATCH" "HG1091_PATCH"
[67] "HG1133_PATCH" "HG1146_PATCH"
[69] "HG115_PATCH" "HG1208_PATCH"
[71] "HG1211_PATCH" "HG122_PATCH"
[73] "HG1257_PATCH" "HG1287_PATCH"
[75] "HG1292_PATCH" "HG1293_PATCH"
[77] "HG1304_PATCH" "HG1308_PATCH"
[79] "HG1322_PATCH" "HG1350_HG959_PATCH"
[81] "HG1423_PATCH" "HG1424_PATCH"
[83] "HG1425_PATCH" "HG1426_PATCH"
[85] "HG142_HG150_NOVEL_TEST" "HG1433_PATCH"
[87] "HG1434_PATCH" "HG1435_PATCH"
[89] "HG1436_HG1432_PATCH" "HG1437_PATCH"
[91] "HG1438_PATCH" "HG1439_PATCH"
[93] "HG1440_PATCH" "HG1441_PATCH"
[95] "HG1442_PATCH" "HG1443_HG1444_PATCH"
[97] "HG144_PATCH" "HG1453_PATCH"
[99] "HG1458_PATCH" "HG1459_PATCH"
[101] "HG1462_PATCH" "HG1463_PATCH"
[103] "HG1472_PATCH" "HG1479_PATCH"
[105] "HG1486_PATCH" "HG1487_PATCH"
[107] "HG1488_PATCH" "HG1490_PATCH"
[109] "HG1497_PATCH" "HG14_PATCH"
[111] "HG1500_PATCH" "HG1501_PATCH"
[113] "HG1502_PATCH" "HG151_NOVEL_TEST"
[115] "HG1591_PATCH" "HG1592_PATCH"
[117] "HG1595_PATCH" "HG1699_PATCH"
[119] "HG174_HG254_PATCH" "HG183_PATCH"
[121] "HG185_PATCH" "HG186_PATCH"
[123] "HG193_PATCH" "HG19_PATCH"
[125] "HG237_PATCH" "HG243_PATCH"
[127] "HG256_PATCH" "HG271_PATCH"
[129] "HG27_PATCH" "HG280_PATCH"
[131] "HG281_PATCH" "HG299_PATCH"
[133] "HG29_PATCH" "HG305_PATCH"
[135] "HG306_PATCH" "HG311_PATCH"
[137] "HG325_PATCH" "HG329_PATCH"
[139] "HG339_PATCH" "HG344_PATCH"
[141] "HG348_PATCH" "HG357_PATCH"
[143] "HG375_PATCH" "HG385_PATCH"
[145] "HG388_HG400_PATCH" "HG414_PATCH"
[147] "HG417_PATCH" "HG418_PATCH"
[149] "HG444_PATCH" "HG480_HG481_PATCH"
[151] "HG497_PATCH" "HG506_HG507_HG1000_PATCH"
[153] "HG50_PATCH" "HG531_PATCH"
[155] "HG536_PATCH" "HG544_PATCH"
[157] "HG686_PATCH" "HG706_PATCH"
[159] "HG729_PATCH" "HG730_PATCH"
[161] "HG736_PATCH" "HG745_PATCH"
[163] "HG747_PATCH" "HG748_PATCH"
[165] "HG75_PATCH" "HG79_PATCH"
[167] "HG7_PATCH" "HG858_PATCH"
[169] "HG865_PATCH" "HG871_PATCH"
[171] "HG873_PATCH" "HG883_PATCH"
[173] "HG905_PATCH" "HG944_PATCH"
[175] "HG946_PATCH" "HG953_PATCH"
[177] "HG957_PATCH" "HG962_PATCH"
[179] "HG971_PATCH" "HG979_PATCH"
[181] "HG987_PATCH" "HG989_PATCH"
[183] "HG990_PATCH" "HG991_PATCH"
[185] "HG996_PATCH" "HG998_1_PATCH"
[187] "HG998_2_PATCH" "HG999_1_PATCH"
[189] "HG999_2_PATCH" "HSCHR10_1_CTG2"
[191] "HSCHR10_1_CTG5" "HSCHR12_1_CTG1"
[193] "HSCHR12_1_CTG2_1" "HSCHR12_1_CTG5"
[195] "HSCHR12_2_CTG2" "HSCHR12_2_CTG2_1"
[197] "HSCHR12_3_CTG2_1" "HSCHR15_1_CTG4"
[199] "HSCHR15_1_CTG8" "HSCHR16_1_CTG3_1"
[201] "HSCHR16_2_CTG3_1" "HSCHR17_1"
[203] "HSCHR17_1_CTG1" "HSCHR17_1_CTG4"
[205] "HSCHR17_2_CTG4" "HSCHR17_3_CTG4"
[207] "HSCHR17_4_CTG4" "HSCHR17_5_CTG4"
[209] "HSCHR17_6_CTG4" "HSCHR18_1_CTG1_1"
[211] "HSCHR18_1_CTG2_1" "HSCHR18_2_CTG2"
[213] "HSCHR18_2_CTG2_1" "HSCHR19LRC_COX1_CTG1"
[215] "HSCHR19LRC_COX2_CTG1" "HSCHR19LRC_LRC_I_CTG1"
[217] "HSCHR19LRC_LRC_J_CTG1" "HSCHR19LRC_LRC_S_CTG1"
[219] "HSCHR19LRC_LRC_T_CTG1" "HSCHR19LRC_PGF1_CTG1"
[221] "HSCHR19LRC_PGF2_CTG1" "HSCHR19_1_CTG3"
[223] "HSCHR19_1_CTG3_1" "HSCHR19_2_CTG3"
[225] "HSCHR19_3_CTG3" "HSCHR1_1_CTG31"
[227] "HSCHR1_2_CTG31" "HSCHR1_3_CTG31"
[229] "HSCHR20_1_CTG1" "HSCHR21_2_CTG1_1"
[231] "HSCHR21_3_CTG1_1" "HSCHR21_4_CTG1_1"
[233] "HSCHR22_1_CTG1" "HSCHR22_1_CTG2"
[235] "HSCHR22_2_CTG1" "HSCHR2_1_CTG1"
[237] "HSCHR2_1_CTG12" "HSCHR2_2_CTG12"
[239] "HSCHR3_1_CTG1" "HSCHR3_1_CTG2_1"
[241] "HSCHR4_1" "HSCHR4_1_CTG12"
[243] "HSCHR4_1_CTG6" "HSCHR4_2_CTG9"
[245] "HSCHR5_1_CTG1" "HSCHR5_1_CTG2"
[247] "HSCHR5_1_CTG5" "HSCHR5_2_CTG1"
[249] "HSCHR5_3_CTG1" "HSCHR6_1_CTG5"
[251] "HSCHR6_MHC_APD" "HSCHR6_MHC_COX"
[253] "HSCHR6_MHC_DBB" "HSCHR6_MHC_MANN"
[255] "HSCHR6_MHC_MCF" "HSCHR6_MHC_QBL"
[257] "HSCHR6_MHC_SSTO" "HSCHR7_1_CTG6"
[259] "HSCHR9_1_CTG1" "HSCHR9_1_CTG35"
[261] "HSCHR9_2_CTG35" "HSCHR9_3_CTG35"
[263] "LRG_123" "LRG_162"
[265] "LRG_183" "LRG_187"
[267] "LRG_239" "LRG_311"
[269] "LRG_415" "LRG_93"
[271] "MT" "X"
[273] "Y"
>
> ## Get all supported mappings for the organism of the EnsDb.
> supportedSeqlevelsStyles(edb)
NULL
>
> ## Change the seqlevels to UCSC style.
> seqlevelsStyle(edb) <- "UCSC"
> seqlevels(edb)
[1] "chr1" "chr10"
[3] "chr11" "chr12"
[5] "chr13" "chr14"
[7] "chr15" "chr16"
[9] "chr17" "chr18"
[11] "chr19" "chr2"
[13] "chr20" "chr21"
[15] "chr22" "chr3"
[17] "chr4" "chr5"
[19] "chr6" "chr7"
[21] "chr8" "chr9"
[23] "GL000191.1" "GL000192.1"
[25] "GL000193.1" "GL000194.1"
[27] "GL000195.1" "GL000196.1"
[29] "GL000199.1" "GL000201.1"
[31] "GL000204.1" "GL000205.1"
[33] "GL000209.1" "GL000211.1"
[35] "GL000212.1" "GL000213.1"
[37] "GL000215.1" "GL000216.1"
[39] "GL000218.1" "GL000219.1"
[41] "GL000220.1" "GL000221.1"
[43] "GL000222.1" "GL000223.1"
[45] "GL000224.1" "GL000225.1"
[47] "GL000228.1" "GL000229.1"
[49] "GL000230.1" "GL000231.1"
[51] "GL000233.1" "GL000236.1"
[53] "GL000237.1" "GL000240.1"
[55] "GL000241.1" "GL000242.1"
[57] "GL000243.1" "GL000247.1"
[59] "HG1007_PATCH" "HG1032_PATCH"
[61] "HG104_HG975_PATCH" "HG1063_PATCH"
[63] "HG1074_PATCH" "HG1079_PATCH"
[65] "HG1082_HG167_PATCH" "HG1091_PATCH"
[67] "HG1133_PATCH" "HG1146_PATCH"
[69] "HG115_PATCH" "HG1208_PATCH"
[71] "HG1211_PATCH" "HG122_PATCH"
[73] "HG1257_PATCH" "HG1287_PATCH"
[75] "HG1292_PATCH" "HG1293_PATCH"
[77] "HG1304_PATCH" "HG1308_PATCH"
[79] "HG1322_PATCH" "HG1350_HG959_PATCH"
[81] "HG1423_PATCH" "HG1424_PATCH"
[83] "HG1425_PATCH" "HG1426_PATCH"
[85] "HG142_HG150_NOVEL_TEST" "HG1433_PATCH"
[87] "HG1434_PATCH" "HG1435_PATCH"
[89] "HG1436_HG1432_PATCH" "HG1437_PATCH"
[91] "HG1438_PATCH" "HG1439_PATCH"
[93] "HG1440_PATCH" "HG1441_PATCH"
[95] "HG1442_PATCH" "HG1443_HG1444_PATCH"
[97] "HG144_PATCH" "HG1453_PATCH"
[99] "HG1458_PATCH" "HG1459_PATCH"
[101] "HG1462_PATCH" "HG1463_PATCH"
[103] "HG1472_PATCH" "HG1479_PATCH"
[105] "HG1486_PATCH" "HG1487_PATCH"
[107] "HG1488_PATCH" "HG1490_PATCH"
[109] "HG1497_PATCH" "HG14_PATCH"
[111] "HG1500_PATCH" "HG1501_PATCH"
[113] "HG1502_PATCH" "HG151_NOVEL_TEST"
[115] "HG1591_PATCH" "HG1592_PATCH"
[117] "HG1595_PATCH" "HG1699_PATCH"
[119] "HG174_HG254_PATCH" "HG183_PATCH"
[121] "HG185_PATCH" "HG186_PATCH"
[123] "HG193_PATCH" "HG19_PATCH"
[125] "HG237_PATCH" "HG243_PATCH"
[127] "HG256_PATCH" "HG271_PATCH"
[129] "HG27_PATCH" "HG280_PATCH"
[131] "HG281_PATCH" "HG299_PATCH"
[133] "HG29_PATCH" "HG305_PATCH"
[135] "HG306_PATCH" "HG311_PATCH"
[137] "HG325_PATCH" "HG329_PATCH"
[139] "HG339_PATCH" "HG344_PATCH"
[141] "HG348_PATCH" "HG357_PATCH"
[143] "HG375_PATCH" "HG385_PATCH"
[145] "HG388_HG400_PATCH" "HG414_PATCH"
[147] "HG417_PATCH" "HG418_PATCH"
[149] "HG444_PATCH" "HG480_HG481_PATCH"
[151] "HG497_PATCH" "HG506_HG507_HG1000_PATCH"
[153] "HG50_PATCH" "HG531_PATCH"
[155] "HG536_PATCH" "HG544_PATCH"
[157] "HG686_PATCH" "HG706_PATCH"
[159] "HG729_PATCH" "HG730_PATCH"
[161] "HG736_PATCH" "HG745_PATCH"
[163] "HG747_PATCH" "HG748_PATCH"
[165] "HG75_PATCH" "HG79_PATCH"
[167] "HG7_PATCH" "HG858_PATCH"
[169] "HG865_PATCH" "HG871_PATCH"
[171] "HG873_PATCH" "HG883_PATCH"
[173] "HG905_PATCH" "HG944_PATCH"
[175] "HG946_PATCH" "HG953_PATCH"
[177] "HG957_PATCH" "HG962_PATCH"
[179] "HG971_PATCH" "HG979_PATCH"
[181] "HG987_PATCH" "HG989_PATCH"
[183] "HG990_PATCH" "HG991_PATCH"
[185] "HG996_PATCH" "HG998_1_PATCH"
[187] "HG998_2_PATCH" "HG999_1_PATCH"
[189] "HG999_2_PATCH" "HSCHR10_1_CTG2"
[191] "HSCHR10_1_CTG5" "HSCHR12_1_CTG1"
[193] "HSCHR12_1_CTG2_1" "HSCHR12_1_CTG5"
[195] "HSCHR12_2_CTG2" "HSCHR12_2_CTG2_1"
[197] "HSCHR12_3_CTG2_1" "HSCHR15_1_CTG4"
[199] "HSCHR15_1_CTG8" "HSCHR16_1_CTG3_1"
[201] "HSCHR16_2_CTG3_1" "HSCHR17_1"
[203] "HSCHR17_1_CTG1" "HSCHR17_1_CTG4"
[205] "HSCHR17_2_CTG4" "HSCHR17_3_CTG4"
[207] "HSCHR17_4_CTG4" "HSCHR17_5_CTG4"
[209] "HSCHR17_6_CTG4" "HSCHR18_1_CTG1_1"
[211] "HSCHR18_1_CTG2_1" "HSCHR18_2_CTG2"
[213] "HSCHR18_2_CTG2_1" "HSCHR19LRC_COX1_CTG1"
[215] "HSCHR19LRC_COX2_CTG1" "HSCHR19LRC_LRC_I_CTG1"
[217] "HSCHR19LRC_LRC_J_CTG1" "HSCHR19LRC_LRC_S_CTG1"
[219] "HSCHR19LRC_LRC_T_CTG1" "HSCHR19LRC_PGF1_CTG1"
[221] "HSCHR19LRC_PGF2_CTG1" "HSCHR19_1_CTG3"
[223] "HSCHR19_1_CTG3_1" "HSCHR19_2_CTG3"
[225] "HSCHR19_3_CTG3" "HSCHR1_1_CTG31"
[227] "HSCHR1_2_CTG31" "HSCHR1_3_CTG31"
[229] "HSCHR20_1_CTG1" "HSCHR21_2_CTG1_1"
[231] "HSCHR21_3_CTG1_1" "HSCHR21_4_CTG1_1"
[233] "HSCHR22_1_CTG1" "HSCHR22_1_CTG2"
[235] "HSCHR22_2_CTG1" "HSCHR2_1_CTG1"
[237] "HSCHR2_1_CTG12" "HSCHR2_2_CTG12"
[239] "HSCHR3_1_CTG1" "HSCHR3_1_CTG2_1"
[241] "HSCHR4_1" "HSCHR4_1_CTG12"
[243] "HSCHR4_1_CTG6" "HSCHR4_2_CTG9"
[245] "HSCHR5_1_CTG1" "HSCHR5_1_CTG2"
[247] "HSCHR5_1_CTG5" "HSCHR5_2_CTG1"
[249] "HSCHR5_3_CTG1" "HSCHR6_1_CTG5"
[251] "HSCHR6_MHC_APD" "HSCHR6_MHC_COX"
[253] "HSCHR6_MHC_DBB" "HSCHR6_MHC_MANN"
[255] "HSCHR6_MHC_MCF" "HSCHR6_MHC_QBL"
[257] "HSCHR6_MHC_SSTO" "HSCHR7_1_CTG6"
[259] "HSCHR9_1_CTG1" "HSCHR9_1_CTG35"
[261] "HSCHR9_2_CTG35" "HSCHR9_3_CTG35"
[263] "LRG_123" "LRG_162"
[265] "LRG_183" "LRG_187"
[267] "LRG_239" "LRG_311"
[269] "LRG_415" "LRG_93"
[271] "chrM" "chrX"
[273] "chrY"
Warning message:
In .formatSeqnameByStyleFromQuery(x, sn, ifNotFound) :
More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: UCSC!) Returning the orginal seqnames for these.
>
> ## Change the option ensembldb.seqnameNotFound to return NA in case
> ## the seqname can not be mapped form Ensembl to UCSC.
> options(ensembldb.seqnameNotFound=NA)
>
> seqlevels(edb)
[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" NA NA NA NA NA
[28] NA NA NA NA NA NA NA NA NA
[37] NA NA NA NA NA NA NA NA NA
[46] NA NA NA NA NA NA NA NA NA
[55] NA NA NA NA NA NA NA NA NA
[64] NA NA NA NA NA NA NA NA NA
[73] NA NA NA NA NA NA NA NA NA
[82] NA NA NA NA NA NA NA NA NA
[91] NA NA NA NA NA NA NA NA NA
[100] NA NA NA NA NA NA NA NA NA
[109] NA NA NA NA NA NA NA NA NA
[118] NA NA NA NA NA NA NA NA NA
[127] NA NA NA NA NA NA NA NA NA
[136] NA NA NA NA NA NA NA NA NA
[145] NA NA NA NA NA NA NA NA NA
[154] NA NA NA NA NA NA NA NA NA
[163] NA NA NA NA NA NA NA NA NA
[172] NA NA NA NA NA NA NA NA NA
[181] NA NA NA NA NA NA NA NA NA
[190] NA NA NA NA NA NA NA NA NA
[199] NA NA NA NA NA NA NA NA NA
[208] NA NA NA NA NA NA NA NA NA
[217] NA NA NA NA NA NA NA NA NA
[226] NA NA NA NA NA NA NA NA NA
[235] NA NA NA NA NA NA NA NA NA
[244] NA NA NA NA NA NA NA NA NA
[253] NA NA NA NA NA NA NA NA NA
[262] NA NA NA NA NA NA NA NA NA
[271] "chrM" "chrX" "chrY"
Warning message:
In .formatSeqnameByStyleFromQuery(x, sn, ifNotFound) :
More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: UCSC!) Returning NA for these.
>
> ## Restoring the original setting.
> options(ensembldb.seqnameNotFound="ORIGINAL")
>
>
> ## Integrate Ensembl based annotations with a BSgenome package that is based on
> ## UCSC style seqnames.
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> bsg <- BSgenome.Hsapiens.UCSC.hg19
>
> ## Get the genome version
> unique(genome(bsg))
[1] "hg19"
> unique(genome(edb))
[1] "GRCh37"
Warning message:
In .formatSeqnameByStyleFromQuery(x, sn, ifNotFound) :
More than 5 seqnames with seqlevels style of the database (Ensembl) could not be mapped to the seqlevels style: UCSC!) Returning the orginal seqnames for these.
> ## Although differently named, both represent genome build GRCh37.
>
> ## Extract the full transcript sequences of all lincRNAs encoded on chromsome Y.
> yTxSeqs <- extractTranscriptSeqs(bsg, exonsBy(edb, "tx",
+ filter=list(SeqnameFilter("chrY"),
+ GenebiotypeFilter("lincRNA"))))
> yTxSeqs
A DNAStringSet instance of length 66
width seq names
[1] 910 TGTCTGTCAGAGCTGTCAGCCTG...TAAACACTGGTATATTTCTGTT ENST00000250776
[2] 910 TGTCTGTCAGAGCTGTCAGCCTG...TAAACACTGGTATATTTCTGTT ENST00000250805
[3] 837 GATGGAGCAAGAATCATCTTGTA...CCTACCAGCCAAAAAAAAAGAA ENST00000253470
[4] 491 GATCATGAGACTATCCTGTGTAT...AAAGCAGTGAAATATTTCTGTT ENST00000253838
[5] 1367 GAGCAGTGTCCTCACGCATTGGA...CTGAAAGATTTCTGTTCCTGAA ENST00000276770
... ... ...
[62] 1483 AGAAAAAGGAAAAAGGCAGATAT...GTGTGATGAAAGAGAAATCTGA ENST00000510613
[63] 983 TGGGGGACCTCCCTTGGGAGATC...TCCCTCCTTAGTGAACAACTGC ENST00000527562
[64] 387 ATGCACCTCCACAGAGGTCTCCT...CAAAGTATCTGTCCCAAAATGA ENST00000538537
[65] 398 CAGCCGGGTTCAATGCGCCATAT...AGTATTTGCCGTTGGTGATTCA ENST00000543097
[66] 2666 CATGGCTAAGTGCCCGGGTTCGT...ATTAAATTGTAAATATTTAAAA ENST00000566193
>
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and