R: Find the position in coding sequence for each variation.

Positionincoding {customProDB}

R Documentation

Find the position in coding sequence for each variation.

Description

For those variations labeled with "Coding", positionincoding() function computes the position of variation in the coding sequence of each transcript.

Usage

  Positionincoding(Vars, exon, dbsnp = NULL, COSMIC = NULL,
    ...)

Arguments

`Vars`	a GRanges object of variations
`exon`	a dataframe of exon annotations for protein coding transcripts.
`dbsnp`	provide a GRanges object of known dbsnp information to include dbsnp evidence into the output table, default is NULL.
`COSMIC`	provide a GRanges object of known COSMIC information to include COSMIC evidence into the output table, default is NULL.
`...`	additional arguments

Details

this function prepares input data frame for aaVariation().

Value

a data frame containing the position in coding sequence for each variation

Author(s)

Xiaojing Wang

Examples

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

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"))
load(system.file("extdata/refseq", "cosmic.RData",
    package="customProDB"))
postable_snv <- Positionincoding(SNVvcf, exon, dbsnpinCoding, COSMIC=cosmic)

[Package customProDB version 1.20.2 Index]