bacsnp.filter: Filtering SNP frequency dataframe

In wennj/bacsnp: Analyzing single nucleotide polymorphisms from baculovirus sequencing data

Filtering SNP frequency dataframe

Description

Filtering SNP frequency dataframe

Usage

bacsnp.filter(vcfdf, min.abs.cov = 0, min.abs.alt = 0,
  min.rel.alt = 0)

Arguments

vcfdf	A dataframe with SNP frequencies. Data was created with vcf_transformation.
min.abs.cov	The minimal absolute coverage (COV) that is required to consider SNP positions. All positions with a miniam absolute coverage below this value will be removed.
min.abs.alt	An absolute value for the minimal number of occurances of an alternative nucleotide.
min.rel.alt	An relative value for the minimal frequency of an alternative nucleotide.

Value

A vcf dataframe that was filtered by a required minimal total coverage (COV), minimal coverage of alternative nucleotides (COV.ALT) or a minimal relative frequency of the first alterntative (REL.ALT1).

Examples

bacsnp.filter(bac, min.abs.cov = 100)
bacsnp.filter(bac, min.abs.cov = 100, min.abs.alt = 10)
bacsnp.filter(bac, min.abs.cov = 100, min.abs.alt = 10, min.rel.alt = 0.05)
bacsnp.filter(bac, min.rel.alt = 0.05)

wennj/bacsnp documentation built on Oct. 20, 2022, 11:17 p.m.