createMSnset {DAPAR} | R Documentation

## 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 `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')

[Package DAPAR version 1.24.8 Index]