After this
library(RNAseqData.HNRNPC.bam.chr14)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
exByGn <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene")
Rsamtools is loaded but not attached; it's
summarizeOverlaps,GRanges,character-method
is available (maybe it shouldn't be, but that's a different question).
Invoking
summarizeOverlaps(exByGn, fls)
results in
summarizeOverlaps(exByGn, fls)
Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'obeyQname<-' of mode 'function' was not found
with
traceback()
14: get(as.character(FUN), mode = "function", envir = envir)
13: match.fun(FUN)
12: lapply(as.list(X), FUN = FUN, ...)
11: lapply(as.list(X), FUN = FUN, ...)
10: lapply(X, FUN = FUN, ...)
9: lapply(X, FUN = FUN, ...)
8: endoapply(object, "obeyQname<-", value = value)
7: endoapply(object, "obeyQname<-", value = value)
6: `obeyQname<-`(`*tmp*`, value = FALSE)
5: `obeyQname<-`(`*tmp*`, value = FALSE)
4: BamFileList(reads, yieldSize = yieldSize, obeyQname = FALSE,
asMates = !singleEnd)
3: .local(features, reads, mode, ignore.strand, ...)
2: summarizeOverlaps(exByGn, fls)
1: summarizeOverlaps(exByGn, fls)
and the parent.frame() of the environment (where the search at line 14
starts) is IRanges, but should be Rsamtools (where endoapply was invoked).
Martin
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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