init_ann_MQ_Excel: Initialize an annotation Excel file based on a MaxQuant...

In ludgergoeminne/MSqRob: Robust statistical inference for quantitative LC-MS proteomics

Initialize an annotation Excel file based on a MaxQuant peptides.txt file

Description

Creates an Excel file with one column containing the run names of an experiment based on the column names of a MaxQuant peptides.txt file. This function might be a start in constructing the first column of the annatation Excel file, other colunms need to be added manually.

Usage

init_ann_MQ_Excel(file, savepath = NULL,
  output_name = "experimental_annotation", col_name = "run",
  pattern = "Intensity.", remove_pattern = TRUE)

Arguments

file	The name of a MaxQuant peptides.txt file. For more details about how this argument can be specified, see read.table.
savepath	The file path to the directory where you want the output Excel annotation file to be saved. If set to NULL (the default), the Excel file will be saved in the working directory.
output_name	The name of the output Excel annotation file. Defaults to "experimental_annotation".
col_name	The name of the only column created in the Excel file. Defaults to "run".
pattern	A character string containing a regular expression that will be matched to the file's header. The columns matching the expression should be the columns containing the peptide intensity values. Defaults to "Intensity.".
remove_pattern	A logical indicating whether the expression in "pattern" should be removed from the column names in the resulting Excel file. Defaults to TRUE.

Value

An Excel file with one column containing the different run names present in the MaxQuant peptides.txt file and column name col_name.

ludgergoeminne/MSqRob documentation built on Jan. 11, 2023, 1:32 p.m.