
## S3 method for class 'RNAseq':
fetchCoverage(obj, format = c("aln", "bam"),
filename = character(1), filter = srFilter(), type = "SolexaExport",
chr.sel = c(), validity.check = TRUE, chr.map = data.frame(),
ignoreWarnings = FALSE, gapped = TRUE, paired = FALSE,
stranded = FALSE, bp.coverage = FALSE, ...)
RNAseq
objectRNAseq
object. The slot readCoverage
contains a SimpleRleList object representing a list of coverage vectors,
one per chromosome.Rle
ShortRead:readAligned
library("RnaSeqTutorial")
library(BSgenome.Dmelanogaster.UCSC.dm3)
obj <- new('RNAseq',
organismName="Dmelanogaster",
readLength=36L,
chrSize=as.list(seqlengths(Dmelanogaster))
)
obj <- fetchCoverage(
obj,
format="bam",
filename=system.file(
"extdata",
"ACACTG.bam",
package="RnaSeqTutorial")
)
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