OutputVarproseq: Output the variant(SNVs) protein sequences into FASTA format

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

Description

Output the non-synonymous SNVs into FASTA file.

Usage

OutputVarproseq(vartable, proteinseq, outfile, ids, lablersid = FALSE,
  RPKM = NULL, ...)

Arguments

vartable	A data frame which is the output of aaVariation().
proteinseq	A dataframe containing protein ids and the protein sequence.
outfile	Output file name.
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.
RPKM	If includes the RPKM value in the header of each sequence, default is NULL.
...	Additional arguments

Details

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

Value

a FASTA file and a data frame containing 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)
outfile <- paste(tempdir(), '/test_snv.fasta',sep='')
snvproseq <- OutputVarproseq(mtab, proteinseq, outfile, ids, lablersid=TRUE, RPKM=NULL)

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