SWATH2stats (version 1.2.3)

convert4aLFQ: convert4aLFQ: Convert table into the format for aLFQ

Description

This functions selects the columns necessary for the aLFQ R package.

Usage

convert4aLFQ(data, annotation = TRUE)

Arguments

data

A data frame containing the SWATH data in transition-level format

annotation

Option to indicate if the data has been annotated, i.e. if the columns Condition, Replicate, Run are present. If option is set to true it will write a new run_id as a string of the combination of these three columns.

Value

Returns a data frame in the appropriate format for aLFQ.

References

Rosenberger G, Ludwig C, Rost HL, Aebersold R, Malmstrom L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200.

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)
data.aLFQ <- convert4aLFQ(raw)