mbqnLoadFile: Load and preprocess LFQ intensities
In MBQN: Mean/Median-balanced quantile normalization

Description Usage Arguments Details Value Author(s) References See Also Examples

Auxilary function used to load and preprocess LFQ intensities of selected dataset with a PRIDE [1] identifier.

1	mbqnLoadFile(pxd_id, source.path = NULL, file.pattern = "proteingroups")

`pxd_id`	the PRIDE identifier.
`source.path`	pathname where to store and search for the data file, e.g. "proteinGroups.txt"-file; default = NULL uses current working directory.
`file.pattern`	character specifying the kind of dataset for download, e.g. "proteinGroups" or "peptides".

Load proteinGroup.txt file, select all samples with LFQ intensities, remove empty protein features. Apply log2 transform to intensities. This function acquires source code of SafeQuant::parseMaxQuantProteinGroupTxt [2].

SummarizedExperiment with

`data`	data matrix
`pxdid`	PRIDE identifier
`featureAnnotations`	dataframe collecting feature annotations, e.g. protein name, "Potential contaminant", etc..
`ixs`	locical array indicating rows of potential contaminant features, or features identified only by site, reverse.

Ariane Schad

[1] Vizca<c3><ad>no JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H. 2016 update of the PRIDE database and related tools. Nucleic Acids Res. 2016 Jan 1;44(D1): D447-D456. PubMed PMID:26527722.
[2] See "SafeQuant" by Erik Ahrne (2016). SafeQuant: A Toolbox for the Analysis of Proteomics Data. R package version 2.3.1., https://CRAN.R-project.org/package=SafeQuant.

getPXDfile() for downloading data from PRIDE.

## Load LFQ intensities of proteomics data of PXD001584:
library(SummarizedExperiment)
out <- mbqnLoadFile(pxd_id = "PXD001584")
mbqn(assays(out)[["data"]])