disaggregate {SWATH2stats} | R Documentation

## disaggregate: Transforms the SWATH data from a peptide- to a transition-level table.

### Description

If the SWATH data should be analyzed on transition-level the data needs to be tranformed from peptide-level table to a transition-level table (one row per transition instead of one row per peptide). The columns "aggr_Fragment_Annotation" and "aggr_Peak_Area" are disaggregated into the new columns "FragmentIon" and "Intensity". The following columns are renamed if they exist: FullPeptideName -> PeptideSequence, Charge -> PrecursorCharge, Area -> Intensity, Fragment -> FragmentIon, Sequence -> NakedSequence.

### Usage

    disaggregate(data, all.columns = FALSE)

### Arguments

`data` | A data frame containing SWATH data.
`all.columns` | Option that all columns are processed. Otherwise only the typical columns needed for downstream analysis are processed.

### Value

Returns a data frame containing the SWATH data in a transition-level table.

### Author(s)

Peter Blattmann

### Examples

    data("OpenSWATH_data", package="SWATH2stats")
    data("Study_design", package="SWATH2stats")
    data <- sample_annotation(OpenSWATH_data, Study_design)
    data.filtered.decoy <- filter_mscore(data, 0.01)
    raw <- disaggregate(data.filtered.decoy)

[Package SWATH2stats version 1.18.0 Index]