VPA: Variant Pattern Analyzer for next-generation sequencing study

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.

Author
Qiang Hu
Date of publication
2013-08-30 20:22:11
Maintainer
Qiang Hu <huqmail@gmail.com>
License
GPL-2
Version
0.3.6

View on R-Forge

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

Files in this package

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