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

> library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: āBiocGenericsā

The following objects are masked from āpackage:parallelā:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from āpackage:statsā:

    xtabs

The following objects are masked from āpackage:baseā:

    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!


-- 
Sam McInturf

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