createMSnset: Creates an object of class 'MSnSet' from text file

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Creates an object of class MSnSet from text file

Description

Builds an object of class MSnSet from a single tabulated-like file for quantitative and meta-data and a dataframe for the samples description. It differs from the original MSnSet builder which requires three separated files tabulated-like quantitative proteomic data into a MSnSet object, including metadata.

Usage

createMSnset(
  file,
  metadata = NULL,
  indExpData,
  colnameForID = NULL,
  indexForMetacell = NULL,
  logData = FALSE,
  replaceZeros = FALSE,
  pep_prot_data = NULL,
  proteinId = NULL,
  software = NULL
)

Arguments

file	The name of a tab-separated file that contains the data.
metadata	A dataframe describing the samples (in lines).
indExpData	A vector of string where each element is the name of a column in designTable that have to be integrated in the Biobase::fData() table of the MSnSet object.
colnameForID	The name of the column containing the ID of entities (peptides or proteins)
indexForMetacell	xxxxxxxxxxx
logData	A boolean value to indicate if the data have to be log-transformed (Default is FALSE)
replaceZeros	A boolean value to indicate if the 0 and NaN values of intensity have to be replaced by NA (Default is FALSE)
pep_prot_data	A string that indicates whether the dataset is about
proteinId	xxxx
software	xxx

Value

An instance of class MSnSet.

Author(s)

Florence Combes, Samuel Wieczorek

Examples

require(Matrix)
exprsFile <- system.file("extdata", "Exp1_R25_pept.txt", package="DAPARdata")
metadataFile <- system.file("extdata", "samples_Exp1_R25.txt", 
package="DAPARdata")
metadata = read.table(metadataFile, header=TRUE, sep="\t", as.is=TRUE)
indExpData <- c(56:61)
colnameForID <- 'id'
obj <- createMSnset(exprsFile, metadata,indExpData,  colnameForID, 
indexForMetacell = c(43:48), pep_prot_data = "peptide", software = 'maxquant')


exprsFile <- system.file("extdata", "Exp1_R25_pept.txt", package="DAPARdata")
metadataFile <- system.file("extdata", "samples_Exp1_R25.txt", package="DAPARdata")
metadata = read.table(metadataFile, header=TRUE, sep="\t", as.is=TRUE)
indExpData <- c(56:61)
colnameForID <- 'AutoID'
obj <- createMSnset(exprsFile, metadata, indExpData,  colnameForID, 
indexForMetacell = c(43:48), pep_prot_data = "peptide", software = 'maxquant')

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.