mergePeptides {qPLEXanalyzer} | R Documentation

## Merge identical peptides intensities

### Description

Merge identical peptides to single peptide intensity. This function is especially useful for phosphopeptide analysis.

### Usage

    mergePeptides(MSnSetObj, summarizationFunction, annotation, keepCols = NULL)

### Arguments

`MSnSetObj` | MSnSet; an object of class MSnSet
`summarizationFunction` | function; method used to aggregate the peptides. sum, mean or median
`annotation` | data.frame; a data.frame of protein annotation of four columns: "Accessions", "Gene", "Description" and "GeneSymbol"
`keepCols` | a vector of additional columns from fData(MSnSetObj) to keep. either be a numeric vector of column indices or a character vector of column names

### Details

Rows of the intensity matrix with identical peptide sequences are merged by summarising the intensities using `summarizationFunction`.

Columns specified with `keepCols` are retained in the final output. Non-unique entries in different rows are concatenated with ';'.

### Value

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

### 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)
    MSnset_P <- mergePeptides(MSnSet_data, sum, human_anno)

[Package qPLEXanalyzer version 1.10.0 Index]