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Last data update: 2014.03.03

R: Reads one or multiple PAHD template files

readPahdFiles

R Documentation

Reads one or multiple PAHD template files

Description

Reads one or multiple ProteomicsAnnotationHubData dcf files into a matrix that can be processed with PAHD. Commnent lines starting with # will be removed. See ProteomicsAnnotationDataHub() for details.

Usage

readPahdFiles(file)

Arguments

file

A character with one of multiple file names.

Value

A matrix containing

Author(s)

Laurent Gatto

Examples

## example file for the PXD000001 data
f <- list.files(system.file("extdata", package = "ProteomicsAnnotationHubData"),
                full.names = TRUE, pattern = "PXD000001.dcf")
readPahdFiles(f)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(ProteomicsAnnotationHubData)
Loading required package: AnnotationHub
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: AnnotationHubData
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: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

This is ProteomicsAnnotationHubData version 1.2.2 
  Read 'ProteomicsAnnotationHubData()' to get started.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ProteomicsAnnotationHubData/readPahdFiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readPahdFiles
> ### Title: Reads one or multiple PAHD template files
> ### Aliases: readPahdFiles
> 
> ### ** Examples
> 
> ## example file for the PXD000001 data
> f <- list.files(system.file("extdata", package = "ProteomicsAnnotationHubData"),
+                 full.names = TRUE, pattern = "PXD000001.dcf")
> readPahdFiles(f)
     Title                                                           
[1,] "PXD000001: Erwinia carotovora and spiked-in protein fasta file"
[2,] "PXD000001: Peptide-level quantitation data"                    
[3,] "PXD000001: MS-GF+ identiciation data"                          
[4,] "PXD000001: raw mass spectrometry data"                         
     Description                                                                                                                                                                                                                                                                                                                                              
[1,] "Four human TMT spliked-in proteins in an Erwinia carotovora background. Expected reporter ion ratios: Erwinia peptides: 1:1:1:1:1:1; Enolase spike (sp|P00924|ENO1_YEAST): 10:5:2.5:1:2.5:10; BSA spike (sp|P02769|ALBU_BOVIN): 1:2.5:5:10:5:1; PhosB spike (sp|P00489|PYGM_RABIT): 2:2:2:2:1:1; Cytochrome C spike (sp|P62894|CYC_BOVIN): 1:1:1:1:1:2."
[2,] "Four human TMT spliked-in proteins in an Erwinia carotovora background. Expected reporter ion ratios: Erwinia peptides: 1:1:1:1:1:1; Enolase spike (sp|P00924|ENO1_YEAST): 10:5:2.5:1:2.5:10; BSA spike (sp|P02769|ALBU_BOVIN): 1:2.5:5:10:5:1; PhosB spike (sp|P00489|PYGM_RABIT): 2:2:2:2:1:1; Cytochrome C spike (sp|P62894|CYC_BOVIN): 1:1:1:1:1:2."
[3,] "Four human TMT spliked-in proteins in an Erwinia carotovora background. Expected reporter ion ratios: Erwinia peptides: 1:1:1:1:1:1; Enolase spike (sp|P00924|ENO1_YEAST): 10:5:2.5:1:2.5:10; BSA spike (sp|P02769|ALBU_BOVIN): 1:2.5:5:10:5:1; PhosB spike (sp|P00489|PYGM_RABIT): 2:2:2:2:1:1; Cytochrome C spike (sp|P62894|CYC_BOVIN): 1:1:1:1:1:2."
[4,] "Four human TMT spliked-in proteins in an Erwinia carotovora background. Expected reporter ion ratios: Erwinia peptides: 1:1:1:1:1:1; Enolase spike (sp|P00924|ENO1_YEAST): 10:5:2.5:1:2.5:10; BSA spike (sp|P02769|ALBU_BOVIN): 1:2.5:5:10:5:1; PhosB spike (sp|P00489|PYGM_RABIT): 2:2:2:2:1:1; Cytochrome C spike (sp|P62894|CYC_BOVIN): 1:1:1:1:1:2."
     SourceType Recipe                                                     
[1,] "FASTA"    "ProteomicsAnnotationHubData:::PXD000001FastaToAAStringSet"
[2,] "mzTab"    "ProteomicsAnnotationHubData:::PXD000001MzTabToMSnSet"     
[3,] "mzid"     NA                                                         
[4,] "mzML"     NA                                                         
     RDataPath                                                                                                 
[1,] "pride/data/archive/2012/03/PXD000001/erwinia_carotovora.rda"                                             
[2,] "pride/data/archive/2012/03/PXD000001/F063721.dat-MSnSet.rda"                                             
[3,] "pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"
[4,] "pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
     Location_Prefix SourceUrl Species              TaxonomyId
[1,] "S3"            "PRIDE"   "Erwinia carotovora" "554"     
[2,] "S3"            "PRIDE"   "Erwinia carotovora" "554"     
[3,] "S3"            "S3"      "Erwinia carotovora" "554"     
[4,] "PRIDE"         "PRIDE"   "Erwinia carotovora" "554"     
     File                                                                 
[1,] "erwinia_carotovora.fasta"                                           
[2,] "F063721.dat-mztab.txt"                                              
[3,] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"
[4,] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
     DataProvider Maintainer                        RDataClass    DispatchClass
[1,] "PRIDE"      "Laurent Gatto <lg390@cam.ac.uk>" "AAStringSet" "AAStringSet"
[2,] "PRIDE"      "Laurent Gatto <lg390@cam.ac.uk>" "MSnSet"      "MSnSet"     
[3,] "PRIDE"      "Laurent Gatto <lg390@cam.ac.uk>" "mzRident"    "mzRident"   
[4,] "PRIDE"      "Laurent Gatto <lg390@cam.ac.uk>" "mzRpwiz"     "mzRpwiz"    
     Tags                                                 
[1,] "Proteomics, TMT6, LTQ Orbitrap Velos, PMID:23692960"
[2,] "Proteomics, TMT6, LTQ Orbitrap Velos, PMID:23692960"
[3,] "Proteomics, TMT6, LTQ Orbitrap Velos, PMID:23692960"
[4,] "Proteomics, TMT6, LTQ Orbitrap Velos, PMID:23692960"
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> dev.off()
null device 
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