[BioC] examples of

[LiGang]

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)
> 
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