customProDB (version 1.12.0)

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

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, ...)

Arguments

position_tab

a data frame from Positionincoding()

coding

a data frame cotaining coding sequence for each protein.

...

Additional arguments

Value

a data frame containing consequence for each variations.

Details

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

Examples

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

index <- which(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,]