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

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq 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(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)

customProDB documentation built on Nov. 8, 2020, 8:06 p.m.