rtracklayer mystery with ucscTableQuery
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Sigal Blay ▴ 20
@sigal-blay-4114
Last seen 9.6 years ago
library(rtracklayer) genes <- c("uc003wgi.1", "uc010lpn.2", "uc010lpm.1") session <- browserSession() # Search only for the first gene - failed with a warning message > query1 <- ucscTableQuery(session, "knownGene", table="kgXref", names=genes[1]) > t1 <- getTable(query1) Warning message: In read.table(f, sep = "\t", header = TRUE) : incomplete final line found by readTableHeader on '' # If I don't specify the genes, the first one is found > query2 <- ucscTableQuery(session, "knownGene", table="kgXref") > t2<-getTable(query2) > t2[t2[,"kgID"]==genes[1],] # 1st gene found > t2[t2[,"kgID"]==genes[2],] # 2nd gene not found > t2[t2[,"kgID"]==genes[3],] # 3rd gene not found # if I specify the genes, first and second are found, but not the third > query3 <- ucscTableQuery(session, "knownGene", table="kgXref", names = genes) > t3 <- getTable(query3) > t3[t3[,"kgID"]==genes[1],] # 1st gene found > t3[t3[,"kgID"]==genes[2],] # 2nd gene found > t3[t3[,"kgID"]==genes[3],] # 3rd gene not found > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rtracklayer_1.6.0 RCurl_1.3-1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.6.1 Biostrings_2.14.12 BSgenome_1.14.2 IRanges_1.4.14 [5] XML_2.6-0
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@michael-lawrence-3846
Last seen 2.3 years ago
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Hi, I'm not able to reproduce this with the latest stable version (the 1.8.x series). Please try to use that. You'll need to upgrade your R to 2.11. Michael On Thu, Jun 3, 2010 at 4:19 PM, Sigal Blay <sblay@sfu.ca> wrote: > library(rtracklayer) > genes <- c("uc003wgi.1", "uc010lpn.2", "uc010lpm.1") > session <- browserSession() > > > # Search only for the first gene - failed with a warning message > > query1 <- ucscTableQuery(session, "knownGene", table="kgXref", > names=genes[1]) > > t1 <- getTable(query1) > Warning message: > In read.table(f, sep = "\t", header = TRUE) : > incomplete final line found by readTableHeader on '' > > # If I don't specify the genes, the first one is found > > query2 <- ucscTableQuery(session, "knownGene", table="kgXref") > > t2<-getTable(query2) > > > t2[t2[,"kgID"]==genes[1],] # 1st gene found > > t2[t2[,"kgID"]==genes[2],] # 2nd gene not found > > t2[t2[,"kgID"]==genes[3],] # 3rd gene not found > > # if I specify the genes, first and second are found, but not the third > > query3 <- ucscTableQuery(session, "knownGene", table="kgXref", names = > genes) > > t3 <- getTable(query3) > > > t3[t3[,"kgID"]==genes[1],] # 1st gene found > > t3[t3[,"kgID"]==genes[2],] # 2nd gene found > > t3[t3[,"kgID"]==genes[3],] # 3rd gene not found > > > > > sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rtracklayer_1.6.0 RCurl_1.3-1 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.6.1 Biostrings_2.14.12 BSgenome_1.14.2 IRanges_1.4.14 > [5] XML_2.6-0 > > _______________________________________________ > 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]]
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Indeed, it works nicely now, thanks :-) ----- Original Message ----- From: Michael Lawrence <lawrence.michael@gene.com> To: Sigal Blay <sblay at="" sfu.ca=""> Cc: bioconductor at stat.math.ethz.ch Sent: Fri, 4 Jun 2010 18:45:33 -0700 (PDT) Subject: Re: [BioC] rtracklayer mystery with ucscTableQuery Hi, I'm not able to reproduce this with the latest stable version (the 1.8.x series). Please try to use that. You'll need to upgrade your R to 2.11. Michael On Thu, Jun 3, 2010 at 4:19 PM, Sigal Blay <sblay at="" sfu.ca=""> wrote: > library(rtracklayer) > genes <- c("uc003wgi.1", "uc010lpn.2", "uc010lpm.1") > session <- browserSession() > > > # Search only for the first gene - failed with a warning message > > query1 <- ucscTableQuery(session, "knownGene", table="kgXref", > names=genes[1]) > > t1 <- getTable(query1) > Warning message: > In read.table(f, sep = "\t", header = TRUE) : > incomplete final line found by readTableHeader on '' > > # If I don't specify the genes, the first one is found > > query2 <- ucscTableQuery(session, "knownGene", table="kgXref") > > t2<-getTable(query2) > > > t2[t2[,"kgID"]==genes[1],] # 1st gene found > > t2[t2[,"kgID"]==genes[2],] # 2nd gene not found > > t2[t2[,"kgID"]==genes[3],] # 3rd gene not found > > # if I specify the genes, first and second are found, but not the third > > query3 <- ucscTableQuery(session, "knownGene", table="kgXref", names = > genes) > > t3 <- getTable(query3) > > > t3[t3[,"kgID"]==genes[1],] # 1st gene found > > t3[t3[,"kgID"]==genes[2],] # 2nd gene found > > t3[t3[,"kgID"]==genes[3],] # 3rd gene not found > > > > > sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rtracklayer_1.6.0 RCurl_1.3-1 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.6.1 Biostrings_2.14.12 BSgenome_1.14.2 IRanges_1.4.14 > [5] XML_2.6-0 > > _______________________________________________ > 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 >
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