convertToMSnset {qPLEXanalyzer} | R Documentation

## 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)

[Package qPLEXanalyzer version 1.10.0 Index]