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Last data update: 2014.03.03

R: Prepare data for inclusion into AnnotationHub

PAHD	R Documentation

Prepare data for inclusion into AnnotationHub

Description

Reads ProteomicsAnnotationHubData dcf files and prepares them for inclusion into AnnotationHub. See ProteomicsAnnotationDataHub{} for details and an example.

Usage

PAHD(x, resourceDir)

Arguments

`x`	One of mulitple ProteomicsAnnotationHubData dcf files.
`resourceDir`	A `character` containing the directory holding the files (for instance PRIDE). If missing, will be inferred from the first `RDataPath` field of `x`.

Details

Note: Current limitation is that all the files are expected to reside in a single resource directory.

Value

A list of PAHD objects that can be used to prepare and submit data to AnnotationHub. See ProteomicsAnnotationHub() for details.

Author(s)

Laurent Gatto ## example file for the PXD000001 data f <- list.files(system.file("extdata", package = "ProteomicsAnnotationHubData"), full.names = TRUE) PXD000001 <- PAHD(f) length(PXD000001) PXD000001[[1]]