PAHD: Prepare data for inclusion into AnnotationHub

In ProteomicsAnnotationHubData: Transform public proteomics data resources into Bioconductor Data Structures

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]]

ProteomicsAnnotationHubData documentation built on Nov. 8, 2020, 5:58 p.m.