LiGang <luzifer.li at="" ...=""> writes: > > #examples of "ucscTableQuery" in "rtracklayer" is shown below: > > session <- browserSession() > genome(session) <- "mm9" > query <- ucscTableQuery(session, "Conservation", > GenomicRanges(57795963, 57815592, "chr12")) query <- ucscTableQuery(session, "Conservation", GenomicRanges(57795963, 57815592, "12")) "12" should be used rather than "chr12" > > tableNames(query)

LiGang <luzifer.li at="" ...=""> writes: > > LiGang <luzifer.li at="" ...=""> writes: > > > > > #examples of "ucscTableQuery" in "rtracklayer" is shown below: > > > > session <- browserSession() > > genome(session) <- "mm9" > > query <- ucscTableQuery(session, "Conservation", > > GenomicRanges(57795963, 57815592, "chr12")) > > query <- ucscTableQuery(session, "Conservation", > GenomicRanges(57795963, 57815592, "12")) > > "12" should be used rather than "chr12" in fact, there are some confusions about the using of "chrom" as "1" or "chr1" library(rtracklayer) browserSession("UCSC")->session track(session,"cytoBand") #error! #Error in inherits(x, "factor") : object 'outputs' not found # with replacing chromosome "chrX" as "X" will work track(session, "cytoBand", GenomicRanges( start=start(range(session)), end=end(range(session)), chrom=gsub("^chr","",as.character(chrom(range(session)))) ) ) ##above command works > > > > > tableNames(query) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >