A vector of characters indicating the BAM files paths.
annotations
An object of type annotationsSet
containing information on genes.
types
A vector of the same length as bamfiles indicating the type
of data in each file. Example: WT vs MUT or untreated vs treated".
sf
A vector of the same length as bamfiles indicating the
scaling factor to apply on each file. Each coverage value is multiplied
by this factor before being reported. Useful for normalizing coverage
by, e.g., reads per million (RPM).
paired_end
logical indicating whether the bamfiles
contains paired-end data.
as_fragments
logical indicating if paired-end data must paired
and merged to form fragments.
Value
An object of class 'coverageDataSet' containing the coverage for each sample.
The details of the output componets are as follow:
data
A data.table with the following components:
chrom
Gene chromosome.
start
Gene transcription start site.
end
Gene transcription termination site.
name
Gene name.
score
Gene score.
strand
Gene strand.
pos
One based positions of the gene.
...
For each sample, report the depth at each position of the gene per sample.
samples
A list containg the samples' names that are in the coverageDataSet.
providing 
.