artmsAvgIntensityRT: Summarize average intensity and retention time per protein

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

Summarize average intensity and retention time per protein

Description

Input an evidence file from MaxQuant and a file containing a list of proteins of interest (optional). The function will summarize from the evidence file and report back the average intensity, average retention time, and the average caliberated retention time. If a list of proteins is provided, then only those proteins will be summarized and returned.

Usage

artmsAvgIntensityRT(
  evidence_file,
  protein_file = NULL,
  output_file = FALSE,
  verbose = TRUE
)

Arguments

evidence_file	(char) The filepath to the MaxQuant searched data (evidence) file (txt tab delimited file).
protein_file	(char) The file path to a file or vector containing a list of proteins of interest.
output_file	(char) The file name for the results (must have the extension .txt). If empty, then the results will be returned as an R object.
verbose	(logical) TRUE (default) shows function messages

Value

An R object with the results and a file with the results (if the output_file argument is provided). It contains averages of Intensity, Retention Time, Caliberated Retention Time

Examples

ave_int <- artmsAvgIntensityRT(evidence_file = artms_data_ph_evidence)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.