load_MaxQ_data: Load MaxQuant result files

In mathiaskalxdorf/IceR: Requantification of label-free DDA proteomics data pre-analyzed by MaxQuant.

Load MaxQuant result files

Description

Load MaxQuant result files

Usage

load_MaxQ_data(
  path = NA,
  min_pep_count = 1,
  min_pep_count_criteria = c("all", "unique"),
  remove_contaminants = T,
  remove_reverse = T,
  intensity_used = c("LFQ intensity", "iBAQ", "Intensity")
)

Arguments

path	Optional path to folder containing MaxQuant outputs. By default set to NA. In this case a file browser is opened. If path is directly specified, it has to end with \
min_pep_count	Minimal required number of quantified peptides per protein. By default set to 1.
min_pep_count_criteria	Criteria how to count quantified peptides per protein. Either all or only unique peptides are counted. By default set to "all".
remove_contaminants	Boolean value indicating if contaminants should be removed. By default set to T.
remove_reverse	Boolean value indicating if reverse hits should be removed. By default set to T.
intensity_used	Specifying which protein quantification data should be used. Selection between "LFQ intensity", "iBAQ" or "Intensity". By default set to "LFQ intensity". Requires corresponding quantification results to be calculated by MaxQuant and stored in respective columns.

Details

Wrapper function to load and filter MaxQuant results.

Value

List object containing protein and peptide quantification information in sub-lists named Protein_level and Peptide_level, respectively.

mathiaskalxdorf/IceR documentation built on Aug. 1, 2022, 8:03 a.m.