convertToMSnset: Converts proteomics TMT intensity data to MSnSet

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Converts proteomics TMT intensity data to MSnSet

Description

Converts processed TMT peptide intensities to MSnSet

Usage

convertToMSnset(
  ExpObj,
  metadata,
  indExpData,
  Sequences = NULL,
  Accessions,
  type = "peptide",
  rmMissing = TRUE
)

Arguments

ExpObj	data.frame; a data.frame consisting of quantitative peptide intensities and peptide annotation
metadata	data.frame; a data.frame describing the samples
indExpData	numeric; a numeric vector indicating the column indexes of intensities in ExpObj
Sequences	numeric; a numeric value indicating the index of column consisting of peptide sequence in ExpObj
Accessions	numeric; a numeric value indicating the index of column consisting of protein accession in ExpObj
type	character; what type of data set to create, either 'peptide' or 'protein'
rmMissing	logical; TRUE or FALSE to indicate whether to remove missing data or not

Details

This function builds an object of class MSnSet from a dataframe consisting of quantitative proteomics intensities data and a meta-data describing the samples information. This function creates an MSnSet object from the intensities and metadata file. The metadata must contain "SampleName", "SampleGroup", "BioRep" and "TechRep" columns. The function can be used for either peptide intensities or data that has already been summarized to protein level. The type argument should be set to 'protein' for the latter.

Value

An object of class MSnSet (see MSnSet-class) object).

Examples

data(human_anno)
data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, 
                               metadata=exp3_OHT_ESR1$metadata_qPLEX1,
                               indExpData=c(7:16), 
                               Sequences=2, 
                               Accessions=6)

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.