fdata <-
GenomicAlignments::summarizeOverlaps(
features = windows$gr.plus,
reads = bam.files,
mode = "IntersectionStrict",
ignore.strand = FALSE,
inter.feature = ignoreMultiMap,
singleEnd = TRUE,
fragments = FALSE,
preprocess.reads = func,
param = bam_param,
BPPARAM = bp_param)
fdata <-
GenomicAlignments::summarizeOverlaps(
features = windows$gr.plus,
reads = BamFileList(bam.files,asMates = TRUE),
mode = "IntersectionStrict",
ignore.strand = FALSE,
inter.feature = ignoreMultiMap,
singleEnd = FALSE,
fragments = FALSE,
strandMode = 2,
preprocess.reads = func,
param = bam_param,
BPPARAM = bp_param)
wider <-
suppressWarnings({
GenomicAlignments::summarizeOverlaps(
features = neighbors,
reads = BamFileList(bam.files,asMates = TRUE),
mode = "IntersectionStrict",
ignore.strand = FALSE,
inter.feature = FALSE,
singleEnd = FALSE,
fragments = FALSE,
strandMode=2,
preprocess.reads = ppfunc,
param = bamParams,
BPPARAM = bpParams)
})
Would you tell me if this is ok? or if counting reads as paired end will have an effect on the analysis?
Thanks in advance.