filter_loci_by_group_coverage: Filter loci based on coverage threshold per sample per group
In methylSig: MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Description Usage Arguments Details Value Examples

View source: R/filter_loci_by_group_coverage.R

An optional function to remove loci not satisfying coverage thresholds from filter_loci_by_coverage in a minimum number of samples per group.

1	filter_loci_by_group_coverage(bs, group_column, min_samples_per_group)

`bs`	a `BSseq` object.
`group_column`	a `character` string indicating the column of `pData(bs)` to use for determining group membership.
`min_samples_per_group`	a named `integer` vector indicating the minimum number of samples with non-zero coverage required for maintaining a locus.

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)
)