customProDB (version 1.12.0)

Outputproseq: output FASTA format file contains proteins that have expression level above the cutoff

Description

Get the FASTA file of proteins that pass RPKM cutoff. the FASTA ID line contains protein ID, gene ID, HGNC symbol and description

Usage

Outputproseq(rpkm, cutoff = "30%", proteinseq, outfile, ids, ...)

Arguments

rpkm

a numeric vector containing RPKM for each protein

cutoff

cutoff of RPKM value. Two options are available, percentage format or RPKM. By default we use "30 proteins according to their RPKMs.

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

Value

FASTA file contains proteins with RPKM above the cutoff.

Details

by taking the RPKM value as input, the function outputs sequences of the proteins that pass the cutoff.

Examples

load(system.file("extdata/refseq", "exon_anno.RData", package="customProDB"))
load(system.file("extdata/refseq", "proseq.RData", package="customProDB"))
bamFile <- system.file("extdata/bams", "test1_sort.bam",
    package="customProDB")
load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
RPKM <- calculateRPKM(bamFile, exon, proteincodingonly=TRUE, ids)
outf1 <- paste(tempdir(), '/test_rpkm.fasta', sep='')
Outputproseq(RPKM, 1, proteinseq, outf1, ids)