Write a ProteomicsAnnotationHubData template

Description

Writes a simple template in dcf format (like an R package DESCRIPTION file) that, once completed (see ProteomicsAnnotationHub() for details), can be imported with readPahdFiles or directly processed with PAHD. Note that these cdf files support comments (as opposed to DESCRIPTION files). Lines starting with # will be removed when parsed by readPahdFiles.

Usage

writePahdTemplate(filename = "")

Arguments

Value

Use for its side effect of preparing a annotation template.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

Examples

writePahdTemplate()

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.

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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(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/writePahdTemplate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: writePahdTemplate
> ### Title: Write a ProteomicsAnnotationHubData template
> ### Aliases: writePahdTemplate
> 
> ### ** Examples
> 
> writePahdTemplate()
Title: A short title (one line)
Description: A longer description
SourceType: FASTA, mzTab, mzid, mzML, ... (only one).
Recipe: see ProteomicsAnnotationHubData() for details
RDataPath: Path to the file (on destination resource).
Location_Prefix: Location of final file. Either S3 or PRIDE.
SourceUrl: Location of source file. Either S3 or PRIDE.
Species: Genus species
TaxonomyId: Search in http://www.ncbi.nlm.nih.gov/taxonomy
File: Data file name
DataProvider: Orignal data provider, such as PRIDE.
Maintainer: Your name <you@email.edu>
RDataClass: Class of file served through AnnotationHub.
DispatchClass: Dispatch class.
Tags: Useful tags.
See ProteomicsAnnotationHubData() for details.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>