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

Details

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

Value

FASTA file contains proteins with RPKM above the cutoff.

Author(s)

Xiaojing Wang

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(customProDB)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/customProDB/Outputproseq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Outputproseq
> ### Title: output FASTA format file contains proteins that have expression
> ###   level above the cutoff
> ### Aliases: Outputproseq
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>