read2count {metaseqR} | R Documentation |
This function is a helper for the metaseqr
pipeline, for reading SAM/BAM or BED files when a read
counts file is not available.
read2count(targets, annotation, file.type = targets$type, trans.level = "gene", utr.flank = 500, has.all.fields = FALSE, multic = FALSE)
targets |
a named list, the output of
|
annotation |
see the |
file.type |
the type of raw input files. It can be
|
utr.flank |
the number of base pairs to flank the 3' UTR of transcripts when analyzing Quant-Seq data. |
trans.level |
see the |
has.all.fields |
a logical variable indicating if
all annotation fields used by |
multic |
a logical value indicating the presence
of multiple cores. Defaults to |
A data frame with counts for each sample, ready to be
passed to the main metaseqr
pipeline.
Panagiotis Moulos
## Not run: my.targets <- read.targets("my_mm9_study_bam_files.txt") gene.data <- get.annotation("mm9","gene") r2c <- read2count(targets=my.targets, file.type=my.targets$type,annotation=gene.data) gene.counts <- r2c$counts libsize.list <- r2s$libsize ## End(Not run)