read_maxquant: Read CF-MS data from MaxQuant

In fosterlab/CFTK: The Co-Fractionation Toolkit

Description

Read in a 'proteinGroups.txt' file output by MaxQuant, and convert it to a CF-MS chromatogram matrix, in which each protein is a row and each fraction is a column.

Usage

read_maxquant(
  filepath,
  identifiers = c("protein groups", "genes"),
  quant_mode = c("iBAQ", "MS1 intensity", "MaxLFQ", "spectral counts", "ratio")
)

Arguments

filepath	path to the proteinGroups.txt file
identifiers	one of 'protein groups' or 'genes'; if the latter, protein groups will be matched to gene names (using the 'Gene names' column in the proteinGroups file), keeping only the best row per gene when there are redundant gene names)
quant_mode	the protein quantitations to use; one of 'iBAQ', 'MS1 intensity', 'MaxLFQ', 'spectral counts', or 'ratio'. Note that in ratiometric experiments with more than one isotopic label, the output matrix may need to be manually split further (e.g. to separate heavy and medium over light ratios).

Value

a numeric matrix with proteins in rows and fractions in columns, and a 'metadata' attribute containing metadata from the proteinGroups file for each row

fosterlab/CFTK documentation built on Jan. 19, 2021, 10:31 p.m.