Outputaberrant: generate FASTA file containing short INDEL

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

Description

Short insertion/deletion may lead to aberrant proteins in cells. We provide a function to generate FASTA file containing this kind of proteins.

Usage

Outputaberrant(positiontab, outfile, coding, proteinseq, ids, RPKM = NULL,
  ...)

Arguments

positiontab	a data frame which is the output of function Positionincoding() for INDELs.
outfile	output file name
coding	a data frame cotaining coding sequence for each protein.
proteinseq	a data frame cotaining amino acid sequence for each protein.
ids	a dataframe containing gene/transcript/protein id mapping information.
RPKM	if includes the RPKM value in the header of each sequence, default is NULL.
...	Additional arguments.

Details

the function applys the INDEL into the coding sequence, then translates them into protein sequence, terminated by stop codon. Remove the sequences the same as normal ones or as part of normal ones.

Value

FASTA file containing aberrant proteins.

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]

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", "proseq.RData", package="customProDB"))
load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
postable_indel <- Positionincoding(indelvcf, exon)
txlist_indel <- unique(postable_indel$txid)
codingseq_indel <- procodingseq[procodingseq$tx_id %in% txlist_indel, ]
outfile <-  paste(tempdir(), '/test_indel.fasta', sep='')
Outputaberrant(postable_indel, coding=codingseq_indel, 
proteinseq=proteinseq, outfile=outfile, ids=ids)
                

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