aaVariation: get the functional consequencece of SNVs located in coding...

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

Description

Variations can be divided into SNVs and INDELs. By taking the output of positionincoding() as input, aaVariation() function predicts the consequences of SNVs in the harbored transcript, such as synonymous or non-synonymous.

Usage

aaVariation(position_tab, coding, show_progress = FALSE, ...)

Arguments

position_tab	a data frame from Positionincoding()
coding	a data frame cotaining coding sequence for each protein.
show_progress	If true, a progress bar will be shown.
...	Additional arguments

Details

this function predicts the consequence for SNVs. for INDELs, use Outputabberrant().

Value

a data frame containing consequence for each variations.

Author(s)

Xiaojing Wang

Examples

vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
vcf <- InputVcf(vcffile)
table(GenomicRanges::values(vcf[[1]])[['INDEL']])

index <- which(GenomicRanges::values(vcf[[1]])[['INDEL']]==FALSE)
SNVvcf <- vcf[[1]][index]
load(system.file("extdata/refseq", "exon_anno.RData", package="customProDB"))
load(system.file("extdata/refseq", "dbsnpinCoding.RData", package="customProDB"))
load(system.file("extdata/refseq", "procodingseq.RData", package="customProDB"))
postable_snv <- Positionincoding(SNVvcf,exon,dbsnpinCoding)
txlist <- unique(postable_snv$txid)
codingseq <- procodingseq[procodingseq$tx_id %in% txlist,]
mtab <- aaVariation (postable_snv,codingseq)
mtab[1:3,]

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