convert4aLFQ {SWATH2stats} | R Documentation

## Convert table into the format expected by aLFQ.

### Description

This function 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 this is checked. However, this makes the function slow and herewith be omitted.

### Value

Returns a data frame in the appropriate format for aLFQ.

### Author(s)

Peter Blattmann

### Examples

    {
     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- SWATH2stats::sample_annotation(OpenSWATH_data, Study_design, verbose=TRUE)
     data.filtered.decoy <- filter_mscore(data, 0.01)
     raw <- disaggregate(data.filtered.decoy)
     data.aLFQ <- convert4aLFQ(raw)
     }

[Package SWATH2stats version 1.24.0 Index]