OutputVarprocodingseq: Output the variant(SNVs) protein coding sequences

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

Description

Output 'snvprocoding'

Usage

OutputVarprocodingseq(vartable, procodingseq, ids, lablersid = FALSE,
  show_progress = 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.
show_progress	If true, a progress bar will be shown.
...	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(GenomicRanges::values(vcf[[1]])[['INDEL']])
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", "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)

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