customProDB (version 1.12.0)

Outputaberrant: generate FASTA file containing short INDEL

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.

Value

FASTA file containing aberrant proteins.

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.

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]

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)