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

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

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(GenomicRanges::values(vcf[[1]])[['INDEL']])
index <- which(GenomicRanges::values(vcf[[1]])[['INDEL']] == TRUE)
indelvcf <- vcf[[1]][index]

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

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