convert4aLFQ {SWATH2stats} | R Documentation |
This functions selects the columns necessary for the aLFQ R package.
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
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.
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)