| countReadsForDEXSeq {DEXSeq} | R Documentation |
WARNING: This function is deprecated, use summarizedOverlaps from the package GenomicRanges instead.
countReadsForDEXSeq( exonicParts, bamFileList, scanBamParam =
ScanBamParam(), singleEnd = TRUE, ignoreStrand = TRUE,
mode = function(features, reads, ignore.strand,
inter.feature = FALSE) { countOverlaps(features,
reads, ignore.strand = ignoreStrand)})
exonicParts |
An GRanges object. |
bamFileList |
A BamFileList object. |
scanBamParam |
Function ScanBamParam to create a parameter object influencing what fields and which records are imported from a BAM file. |
singleEnd |
Logical. Indicating whether the reads are single-end or paired-end. |
ignoreStrand |
Logical. Indicating whether the strand of the reads should be ignored. Useful for data generated by strand-specific protocols. |
mode |
A function with the method used to count the overlaps to exons. The default allows a read fragment to be counted in two exons, if it overlaps with both of them. |
A GRanges object.
From code kindly provided by Mike Love.
## Not run:
library(GenomicFeatures)
hse <- makeTranscriptDbFromBiomart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
exonicParts <- prepareAnnotationForDEXSeq( hse )
bamDir <- system.file("extdata",package="parathyroidSE",mustWork=TRUE)
fls <- list.files(bamDir, pattern="bam$",full=TRUE)
bamlst <- BamFileList(fls)
SE <- countReadsForDEXSeq( exonicParts, bamlst )
## End(Not run)