Load multiple MaxQuant output files — load_multiple

Load several proteinGroups.txt files from MaxQuant and perform some cleaning steps to prepare the data for combined analysis. If only one file is to be analyzed, use load_maxquant() instead. For automatic loading, place proteinGroups.txt files in subfolders within datadir. 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_multiple_maxquant(
  file = "proteinGroups.txt",
  datadir = "Data",
  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 files are located (default is "Data"). The function performs a recursive search in this directory for all files matching the specified file name.
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 list of data frames containing the MaxQuant data.

Examples

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