OutputsharedPro: Output the sequences of proteins with high expressions in...

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

Description

Output a FASTA file containing shared proteins with expression above cutoff in multiple samples

Usage

  OutputsharedPro(RPKMs, cutoff = "30%",
    share_sample = "50%", proteinseq, outfile, ids, ...)

Arguments

RPKMs	RPKM matrix; row name (protein name) is required.
cutoff	a percentage format cutoff (e.g. '30 a vector with each element as a vlaue cutoff referring to one sample
share_sample	the minimum share sample numbers for proteins which pass the cutoff.
proteinseq	a dataframe containing protein ids and protein sequences
outfile	output file name
ids	a dataframe containing gene/transcript/protein id mapping information.
...	additional arguments

Details

this function takes RPKM matrix as input, users can set two paramteters,cutoff and shared, to generated a consensus expressed database

Value

a FASTA file containing proteins with RPKM above the cutoff in at least certain number of samples

Author(s)

Xiaojing Wang

Examples

path <- system.file("extdata/bams", package="customProDB")
load(system.file("extdata/refseq", "exon_anno.RData", package="customProDB"))
load(system.file("extdata/refseq", "proseq.RData", package="customProDB"))
load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
bamFile<- paste(path, '/', list.files(path, pattern="*bam$"), sep='')
rpkms <- sapply(bamFile,function(x)
            calculateRPKM(x, exon, proteincodingonly=TRUE, ids))
outfile <- paste(tempdir(), '/test_rpkm_share.fasta', sep='')
OutputsharedPro(rpkms, cutoff=1, share_sample=2, proteinseq,
            outfile, ids)

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