[BioC] GenomicRanges BamFileList() not a function anymore?

[James W. MacDonald]

Hi Sam,

On 5/2/2013 4:35 PM, Sam McInturf wrote:
> Bioconductor users,
>     I have been mapping my RNA seq reads using the GenomicRanges package,
> and was doing alright with it until I upgraded to R-3.0.0.  At least I
> assume that the upgrade was the problem.  After loading GenomicRanges the
> function BamFileList() is not longer a function.  As below

IIRC, the BamFileList function has never been in GenomicRanges, instead 
being defined in Rsamtools.

Best,

Jim


>
>> library(GenomicRanges)
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: âBiocGenericsâ
>
> The following objects are masked from âpackage:parallelâ:
>
>      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>      clusterExport, clusterMap, parApply, parCapply, parLapply,
>      parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following object is masked from âpackage:statsâ:
>
>      xtabs
>
> The following objects are masked from âpackage:baseâ:
>
>      anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval,
>      Filter, Find, get, intersect, lapply, Map, mapply, match, mget,
>      order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
>      rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
>      tapply, union, unique, unlist
>
> Loading required package: IRanges
>
>> BamFileList()
> Error: could not find function "BamFileList"
>
> I work on two clusters, and both no longer work.  What am I doing wrong, or
> what is an alternative to this method?  I have been following the
> summerizeOverlaps vignette for mapping.
>
> thanks in advance!
>
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099