filter_loci_by_group_coverage {methylSig} | R Documentation |
An optional function to remove loci not satisfying coverage thresholds from filter_loci_by_coverage
in a minimum number of samples per group.
filter_loci_by_group_coverage(bs, group_column, min_samples_per_group)
bs |
a |
group_column |
a |
min_samples_per_group |
a named |
The filter_loci_by_coverage
function marked locus/sample pairs in the coverage matrix as 0 if said pair had coverage less than minCount
or more than maxCount
. This function enforces a threshold on the minimum number of samples per group required for a locus to be tested in downstream testing functions.
A BSseq
object with only those loci having min_samples_per_group
.
data(BS.cancer.ex, package = 'bsseqData') filter_loci_by_group_coverage( bs = BS.cancer.ex, group_column = 'Type', min_samples_per_group = c('cancer' = 3, 'normal' = 3) )