gefreq: Frequency analysis at gene level

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

Description

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

Usage

gefreq(vcf, method="fisher.test", p=1, level="gene", ref="hg19", ...)

Arguments

vcf	A varlist object.
method	The test method for mutated genes. This must be one of "fisher.test" and "chisq.test".
p	The maximum of the p values.
level	The annotation level for variants. It can be either "gene" (i.e., including intron region) or "exon" only (i.e., without including intron region).
ref	The version of reference genome, e.g. "hg19".
...	More arguments for the test method.

Value

A list contains a dataframe of frequencies between groups and an annotation list of each samples.

frequency	A data frame to list the gene name, variation distribution, variation frequency and p.value of all genes with variants across study groups.
otherfreq	A data frame to list the frequency results of the genes that are not in the specified level.
annotation	A list including gene annotations for the variants of each sample.

Author(s)

Qiang Hu

See Also

vcfreq

Examples

#gefreq(varRes1)

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