[BioC] rtracklayer mystery with ucscTableQuery

[Sigal Blay]

Indeed, it works nicely now, thanks :-)

----- Original Message -----
From: Michael Lawrence <lawrence.michael at 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
>
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