vcfreq: Variant frequency of a varlist

In VPA: Variant Pattern Analyzer for next-generation sequencing study

Description

To summarize the frequency of variants and estimate the statistical significance of frequency difference.

Usage

vcfreq(vcf, method="fisher.test", p=1, ...)

Arguments

vcf	A varlist object.
method	The allele frequency test method to be used. This must be one of "fisher.test" and "chisq.test".
p	The maximum of the p values.
...	More arguments for the test method.

Value

A data frame to list the position, REF, genotypes, variant allele frequencies and p.value of all variants across study groups.

Author(s)

Qiang Hu

See Also

gefreq

Examples

##read example vcf file in data directory.
#vcfreq(varRes1)

VPA documentation built on May 2, 2019, 4:45 p.m.