Remove loci from consideration for differential testing where the groups tested do not have sufficient coverage in enough samples per group. Use after filter_loci_by_coverage(), filter_loci_by_snps(), and a tiling function. Use before differential methylation testing. Optional.
Arguments
bs a BSseq object possibly having passed through prior filtering and tiling functions.
group_column a character corresponding to a column name in colData(bs) with factors to be named in named vector min_per_group.
min_samples_per_group a named integer vector with names corresponding to factors in group_column and values corresponding to the minimum number of samples with non-zero coverage.
Values
A BSseq object with only those loci having min_samples_per_group.
Function call
filter_loci_by_group_coverage(bs, group_column, min_samples_per_group)Description
Remove loci from consideration for differential testing where the groups tested do not have sufficient coverage in enough samples per group. Use after
filter_loci_by_coverage(),filter_loci_by_snps(), and a tiling function. Use before differential methylation testing. Optional.Arguments
bsaBSseqobject possibly having passed through prior filtering and tiling functions.group_columnacharactercorresponding to a column name incolData(bs)with factors to be named in named vectormin_per_group.min_samples_per_groupa namedintegervector with names corresponding to factors ingroup_columnand values corresponding to the minimum number of samples with non-zero coverage.Values
A
BSseqobject with only those loci havingmin_samples_per_group.Tests
Test for correct removal of loci.