VPA: Variant Pattern Analyzer for next-generation sequencing study
Version 0.3.6

VPA (Variant Pattern Analyzer) is a package for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. To install VPA package in Unix-like operation system, the version of R should be >= 2.12.1. To install VPA package in Windows operation system, the version of R should be >=2.14.0.

AuthorQiang Hu
Date of publication2013-08-30 20:22:11
MaintainerQiang Hu <huqmail@gmail.com>
LicenseGPL-2
Version0.3.6
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("VPA", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

filtervcf: Filter variants with user-specified quality criteria
gefreq: Frequency analysis at gene level
getref: Download reference gene annotation
LoadFiltering: To load and filter variants in batch mode
Patterning: Extract variants with user-specified variant pattern
read.vcf: Read VCF file
subvcf: Subset of VCF data
See all...

All man pages Function index File listing

Man pages

filterpos: Filter variants against known SNP dataset
filtervcf: Filter variants with user-specified quality criteria
gefreq: Frequency analysis at gene level
getref: Download reference gene annotation
LoadFiltering: To load and filter variants in batch mode
Patterning: Extract variants with user-specified variant pattern
Pos2Gene: Map sequencing variants to gene
pos2seq: Positions to sequencing calls
read.vcf: Read VCF file
subvcf: Subset of VCF data
vcfreq: Variant frequency of a varlist
VPA-package: Extract variants from VCF data with specified variant...
write.vcf: Write VCF object

Functions

Files

DESCRIPTION
NAMESPACE
R
R/LoadFiltering.R
R/Patterning.R
R/ann.R
R/filterpos.R
R/filtervcf.R
R/gefreq.R
R/pos2seq.R
R/readvcf.R
R/vcfreq.R
R/writevcf.R
inst
inst/NEWS
inst/README
inst/doc
inst/doc/VPA.pdf
inst/extdata
inst/extdata/1151HZ0001.flt.vcf
inst/extdata/1151HZ0001.vcf.gz
inst/extdata/1151HZ0001.vcf.gz.tbi
inst/extdata/1151HZ0002.flt.vcf
inst/extdata/1151HZ0002.vcf.gz
inst/extdata/1151HZ0002.vcf.gz.tbi
inst/extdata/1151HZ0004.flt.vcf
inst/extdata/1151HZ0004.vcf.gz
inst/extdata/1151HZ0004.vcf.gz.tbi
inst/extdata/1151HZ0005.flt.vcf
inst/extdata/1151HZ0005.vcf.gz
inst/extdata/1151HZ0005.vcf.gz.tbi
inst/extdata/1151HZ0006.flt.vcf
inst/extdata/1151HZ0006.vcf.gz
inst/extdata/1151HZ0006.vcf.gz.tbi
inst/extdata/1151HZ0007.flt.vcf
inst/extdata/1151HZ0007.vcf.gz
inst/extdata/1151HZ0007.vcf.gz.tbi
inst/extdata/1KG.vcf.gz
inst/extdata/1KG.vcf.gz.tbi
inst/extdata/dbSNP.bed.gz
inst/extdata/dbSNP.bed.gz.tbi
inst/extdata/index1.txt
inst/extdata/index2.txt
inst/extdata/index3.txt
man
man/LoadFiltering.Rd
man/Patterning.Rd
man/Pos2Gene.Rd
man/VPA-package.Rd
man/filterpos.Rd
man/filtervcf.Rd
man/gefreq.Rd
man/getref.Rd
man/pos2seq.Rd
man/read.vcf.Rd
man/subvcf.Rd
man/vcfreq.Rd
man/write.vcf.Rd
VPA documentation built on May 21, 2017, 12:27 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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