bacsnp.filter: Filtering SNP frequency dataframe

Description Usage Arguments Value Examples

View source: R/snp_filter.R

Description

Filtering SNP frequency dataframe

Usage

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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

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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 July 13, 2020, 1:19 p.m.