count.unknowns-methods: Calculate missing nucleotide frequencies
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Value Examples

A generic function to calculate the missing nucleotide frequencies.

1 2	## S4 method for signature 'GENOME' count.unknowns(object)

object

An object of class "GENOME"

Returned value is a modified object of class "GENOME"

The slot GENOME.class@missing.freqs for the missing frequencies for the whole region.
The slot GENOME.class@region.stats@missing.freqs for the missing frequencies for each SNP in a given region

# GENOME.class <- readData("VCF", format="VCF", include.unknown=TRUE)
# GENOME.class@region.stats
# GENOME.class <- count.unknowns(GENOME.class)
# GENOME.class@missing.freqs
# GENOME.class@region.stats@missing.freqs

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.