Arguments
dirs
Input directories. Usually each sample is in a different
directory, or perhaps each (sample, lane) is a different directory.
sampleNames
sample names, based on the order of dirs.
If NULL either set to basename(dirs) (if unique) or
dirs.
seqnames
The default is to read all BSmooth output files in
dirs. Using this argument, it is possible to restrict this
to only files with names in seqnames (apart from
.cpg.tsv and optionally .gz).
returnRaw
Should the function return the complete information
in the output files?
qualityCutoff
Only use evidence (methylated and unmethylated
evidence) for a given methylation loci, if the base in the read has
a quality greater than this cutoff.
rmZeroCov
Should methylation loci that have zero coverage in
all samples be removed. This will result in a much smaller object
if the data originates from (targeted) capture bisulfite
sequencing.
verbose
Make the function verbose.