disaggregate: Transforms the SWATH data from a peptide- to a...

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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 "Fragmentation" and "Intensity". The following columns are renamed if they exist: FullPeptideName -> PeptideSequence, Charge -> PrecursorCharge, Area -> Intensity, Fragment -> Fragmentation, 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 columns typically 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)
 }

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.