convert4MSstats {SWATH2stats} | R Documentation |
Though SWATH2stats uses very similar format as MSstats, some coercion is required to convert the data into the format for MSstats.
convert4MSstats( data, replace_values = TRUE, replace_colnames = TRUE, replace_unimod = TRUE )
data |
A data frame containing SWATH data. |
replace_values |
Option to indicate if negative and 0 values should be replaced with NA. |
replace_colnames |
Option to indicate if column names should be renamed and columns reduced to the necessary columns for MSstats. |
replace_unimod |
Option to indicate if Unimod Identifier should be replaced from ":" to "_". |
This functions selects the columns necessary for MSstats and renames them if necessary.
The necessary columns are selected and three columns renamed: FullPeptideName -> PeptideSequence Charge -> PrecursorCharge filename -> File
Returns a data frame in the appropriate format for MSstats.
Peter Blattmann
Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305.
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.mapDIA <- convert4MSstats(raw)