init_ann_MQ_Excel: Initialize an annotation Excel file based on a MaxQuant...
In statOmics/MSqRob: Robust statistical inference for quantitative LC-MS proteomics

init_ann_MQ_Excel

R Documentation

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`.