convert4aLFQ {SWATH2stats} | R Documentation

## 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, check_transitions = 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.
`check_transitions` | Option if number of transitions should be checked. As input only transition-level data should be used and therefore the number of transitions can be checked to spot any irregulatirities. However, this makes the function slow.

### Value

Returns a data frame in the appropriate format for aLFQ.

### Author(s)

Peter Blattmann

### 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)

[Package SWATH2stats version 1.14.0 Index]