read.bams-methods: description of function read.bams

In stela2502/StefansExpressionSet: StefansExpressionSet

description of function read.bams

Description

Use most of'StefansExpressionSet'functionallity with minor changes to NGS data (like normalizing)

This package is mainly meant to plot the data - all important quantification or gene

annotation is performed using DEseq functionallity. Read a set of bam files and perform

the quantification (better do that without using this function!)

Usage

read.bams(bamFiles, annotation, GTF.featureType = "exon",
  GTF.attrType = "gene_id", isPairedEnd = FALSE, nthreads = 2,
  as.obj = F)

Arguments

bamFiles	a file containing one file name per line
annotation	the gene level annotation to use
as.obj	if true return the couts object instead of a matrix (default =F)

stela2502/StefansExpressionSet documentation built on April 24, 2023, 8:15 p.m.