convert4MSstats: Get data ready for use by MSstats.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/convert4MSstats.R

Description

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

Usage

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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

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 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)

SWATH2stats documentation built on April 17, 2021, 6:01 p.m.