Load MaxQuant output file — load_maxquant • VolcanoPlotR

Load a proteinGroups.txt file from MaxQuant and perform some cleaning steps to prepare the data for analysis. Proteins that are only identified by site, reverse hits, and potential contaminants are removed, and missing gene and protein names are filled in based on the "Fasta.headers" column. Note: in the case of multiple identified proteins, the first one in the list is kept.

Usage

load_maxquant(
  file = "proteinGroups.txt",
  datadir = "Data",
  filepath = NULL,
  clean = TRUE
)

Arguments

file: character string specifying the name of the MaxQuant output file to load (default is "proteinGroups.txt").
datadir: character string specifying the directory where the MaxQuant output file is located (default is "Data").
filepath: character string specifying the full path to the MaxQuant file. If provided, this will override the file and datadir parameters.
clean: boolean indicating whether to perform cleaning steps on the data (default is TRUE). If TRUE, rows with a "+" in the "Only.identified.by.site", "Reverse", or "Potential.contaminant" columns will be removed, and missing gene and protein names will be filled in based on the "Fasta.headers" column.

Value

A data frame containing the MaxQuant data.

Examples

if (FALSE) { # \dontrun{
load_maxquant()
} # }