load_Requant_data: Load IceR result files

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

Load IceR result files

Description

Load IceR result files

Usage

load_Requant_data(
  path_to_parameter_file = NA,
  path_to_requant_folder = NA,
  file_name_extension = NA,
  path_MaxQ = NA,
  quant_value = c("LFQ", "Total", "Top3"),
  min_feat_count = 1,
  min_feat_count_criteria = c("all", "unique"),
  imputed = T
)

Arguments

path_to_parameter_file	Optional path to IceR parameter file created during IceR run. By default set to NA. In this case a file browser is opened asking for the path to the Parameters.xlsx generated during IceR run.
path_to_requant_folder	Optional path to folder containing IceR outputs. Not required if path_to_parameter_file is defined. By default set to NA. In this case a file browser is opened. If path is directly specified, it has to end with \
file_name_extension	Optional file name extension of IceR output files. Not required if path_to_parameter_file is defined. Only required if path_to_requant_folder directly specified.
path_MaxQ	Optional path to folder containing MaxQuant outputs. Not required if path_to_parameter_file is defined. By default set to NA. In this case a file browser is opened. If path is directly specified, it has to end with \
quant_value	Specifying which protein quantification data should be used. Selection between "LFQ", "Total" or "Top3". By default set to "LFQ".
min_feat_count	Minimal required number of quantified features per protein. By default set to 1.
min_feat_count_criteria	Criteria how to count quantified features per protein. Either all or only unique peptide features are counted. By default set to "all".
imputed	Boolean value indicating if data with noise model based imputation should be used. By default set to T.

Details

Wrapper function to load and filter IceR 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.