Keeps alleles with more than read_filter reads and, if filter_wsaf is
TRUE, a within-sample allele frequency above af_filter.
Usage
filter_allele_table(
allele_table,
group_cols = c("sample_name", "target_name"),
read_filter = 0,
af_filter = 0.01,
filter_wsaf = TRUE
)
Arguments
- allele_table
Allele or resistance marker table with reads.
- group_cols
Columns identifying a locus within a sample, used to
calculate allele frequency.
- read_filter
Minimum reads per allele.
- af_filter
Minimum within-sample allele frequency.
- filter_wsaf
If FALSE, only read_filter is applied.
Value
The filtered table, with the same columns as allele_table.