artmsAvgIntensityRT: Summarize average intensity and retention time per protein

In artMS: Analytical R tools for Mass Spectrometry

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,
  species,
  verbose = TRUE
)

Arguments

evidence_file	(char) The filepath to the MaxQuant searched data (evidence) file (txt tab delimited file).
protein_file	(char) The filepath to a file or vector conatining 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.
species	(char) The species name. Check ?artmsMapUniprot2Entrez for supported species
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,
                                  species = "human")

artMS documentation built on April 14, 2021, 6 p.m.