convert4MSstats: Get data ready for use by MSstats.

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Get data ready for use by MSstats.

Description

Though SWATH2stats uses very similar format as MSstats, some coercion is required to convert the data into the format for MSstats.

Usage

convert4MSstats(
  data,
  replace_values = TRUE,
  replace_colnames = TRUE,
  replace_unimod = TRUE
)

Arguments

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 "_".

Details

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

Value

Returns a data frame in the appropriate format for MSstats.

Author(s)

Peter Blattmann

References

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.

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.mapDIA <- convert4MSstats(raw)

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.