OutputVarprocodingseq: Output the variant(SNVs) protein coding sequences

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Description

Output 'snvprocoding'

Usage

OutputVarprocodingseq(vartable, procodingseq, ids, lablersid = FALSE, ...)

Arguments

vartable	A data frame which is the output of aaVariation().
procodingseq	A dataframe containing protein ids and coding sequence for the protein.
ids	A dataframe containing gene/transcript/protein id mapping information.
lablersid	If includes the dbSNP rsid in the header of each sequence, default is FALSE. Must provide dbSNP information in function Positionincoding() if put TRUE here.
...	Additional arguments

Details

This function uses the output of aaVariation() as input, introduces the nonsynonymous variation into the protein database.

Value

a data frame containing protein coding sequence proteins with single nucleotide 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']] == 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", "ids.RData", package="customProDB"))
load(system.file("extdata/refseq", "proseq.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)
OutputVarprocodingseq(mtab, codingseq, ids, lablersid=TRUE)

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