R Graphical Manual

Browse All

Last data update: 2014.03.03

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

OutputsharedPro

R Documentation

Output the sequences of proteins with high expressions in multiple samples.

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)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/OutputsharedPro.Rd_%03d_medium.png", width=480, height=480)
> ### Name: OutputsharedPro
> ### Title: Output the sequences of proteins with high expressions in
> ###   multiple samples.
> ### Aliases: OutputsharedPro
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>