convert4aLFQ: Convert table into the format expected by aLFQ.
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

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

1	convert4aLFQ(data, annotation = TRUE, check_transitions = TRUE)

`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.

Returns a data frame in the appropriate format for aLFQ.

Peter Blattmann

{
 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)
 }