pp.msms.data: Spectral counts matrix pre-processing

In msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

Description

Given a MSnSet, possibly subsetted from a bigger dataset, removes the all zero rows, and those whith row names (accessions) ending with '-R' in the corresponding expression matrix. NAs are replaced by zeroes, as usually a NA in a spectral counts matrix corresponds to a proteint not identified in a sample.

Usage

pp.msms.data(msnset)

Arguments

msnset

A MSnSet with spectral counts in the expression matrix.

Details

An '-R' protein corresponds to an artefactual identification.
Rows with all zeros are uninformative and may give rise to errors in the analysis.
A NA is understood as a unidintified protein in a sample.

Value

Returns an updated MSnSet object.
Its processingData slot shows that the object has been processed by pp.msms.data

Author(s)

Josep Gregori

See Also

MSnSet

Examples

data(msms.dataset)
dim(msms.dataset)
msnset <- pp.msms.data(msms.dataset)
dim(msnset)

msmsEDA documentation built on Nov. 8, 2020, 6:55 p.m.