getVariantAnnotation: Get genome annotations for variants called in one or more VCF...

In chambm/customProDB: Generate customized protein databases from NGS data for proteomics search

Description

Get genome annotations for variants called in one or more VCF files. Each sample is called separately so that variants on the same codon are handled properly. This is a convenience function which calls OutputVarprocodingseq, OutputVarproseq, Outputaberrant, and OutputNovelJun.

Usage

getVariantAnnotation(vcfFilepaths, ids, exon_anno, proteinseq, procodingseq,
  dbsnpinCoding = NULL, cosmic = NULL)

Arguments

vcfFilepaths	one or more VCF files to create variant proteins
ids	a dataframe mapping between gene/transcript/protein ids
exon_anno	a dataframe of exon annotations for each protein coding transcript
proteinseq	a dataframe of reference amino acid sequences for each protein
procodingseq	a dataframe of reference coding sequences for each protein coding transcript
dbsnpinCoding	a GRanges object of dbSNP variants to include in the output tables; default is NULL
cosmic	a GRanges object of COSMIC variants to include in the output tables; default is NULL

Value

A list of annotation tables with named members:

variantTable

describes the SNP variants and their coding consequences

snvprocoding

the CDS sequences for the variant proteins from SNPs

snvproseq

the translated sequences for the variant proteins from SNPs

indelprocoding

the CDS sequences for the variant proteins from INDELs

indelproseq

the translated sequences for the variant proteins from INDELs

Examples

load(system.file("extdata/refseq", "exon_anno.RData", package="customProDB"))
load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
load(system.file("extdata/refseq", "procodingseq.RData", package="customProDB"))
load(system.file("extdata/refseq", "proseq.RData", package="customProDB"))
load(system.file("extdata/refseq", "dbsnpinCoding.RData", package="customProDB"))
load(system.file("extdata/refseq", "cosmic.RData", package="customProDB"))
vcfFilepath = system.file("extdata/vcfs", "test1.vcf", package="customProDB")

variantAnnotation = getVariantAnnotation(vcfFilepath, ids, exon,
                                         proteinseq, procodingseq,
                                         dbsnpinCoding, cosmic)
head(variantAnnotation$variantTable)
head(variantAnnotation$snvprocoding)
head(variantAnnotation$snvproseq)
head(variantAnnotation$indelprocoding)
head(variantAnnotation$indelproseq)

chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.