customProDB (version 1.12.0)

Positionincoding: 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

Value

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

Details

this function prepares input data frame for aaVariation().

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)