htseqCount: Calls the htseq-count executable to count input reads on...

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Calls the htseq-count executable to count input reads on features.

Usage

## Default S3 method:
htseqCount(pathnameS, gff, orderedBy=c("none", "position", "name"),
  sortByName=c("always", "auto"), optionsVec=c(`-s` = "no", `-a` = "10"), ...,
  pathnameD=NULL, command="htseq-count", verbose=FALSE)

Arguments

pathnameS	An input BAM or SAM file containing aligned reads.
gff	The gene feature file, in GFF/GTF format.
orderedBy	A character string specifying how the input file has been sorted, if at all.
sortByName	A character string specifying when the BAM/SAM file should be sorted by name.
optionsVec	A named character vector of options to htseq-count.
...	(Not used)
pathnameD	(optional) destination file to save htseq-count output.
command	A character string specifying the name of the executable.
verbose	See Verbose.

Value

Returns what systemHTSeqCount() returns.

Backward compatibility

htseq-count (< 0.6.0) requires (i) a SAM file as input that (ii) is sorted by name. However, this method will take care of that internally, iff needed. That is, it will created a temporary SAM file that is sorted by query name before passing it to htseq-count.

Author(s)

Taku Tokuyasu, Henrik Bengtsson

References

[1] S Anders, TP Pyl, W Huber, HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv 2014. doi: 10.1101/002824.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.