VPA-package: Extract variants from VCF data with specified variant...
In VPA: Variant Pattern Analyzer for next-generation sequencing study

Description Details Author(s) Examples

VPA (Variant Pattern Analyzer) is a package for prioritizing variants with user-specified frequency pattern from multiple study subjects in next-generation sequencing study. The package starts from individual files of sequence and variant calls and the extract variants with user-specified frequency pattern across the study subjects of interest. The frequency pattern can be analyzed at both variant level and gene level, and functions are provided to assess the statistical significance of observed frequency difference.

Package:	VPA
Type:	Package
Version:	0.3.5
Date:	2012-04-23
License:	GPL-2
LazyLoad:	yes

Qiang Hu

Maintainer: Qiang Hu <huqmail@gmail.com>

#setwd(system.file("extdata", package="VPA"))
#varflt <- LoadFiltering(file="index1.txt", filtering=TRUE)
#pattern <- cbind(A=c(1/4,1), B=c(0,0))
#varRes1 <- Patterning(varflt, pattern)

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