artmsMsstatsSummary: Summarize the MSStats results and data quantification

In artMS: Analytical R tools for Mass Spectrometry

Description

Converts the MSStats results file to wide format (unique Protein ID and columns are the comparisons), as well as adds BioReplicate information about

• the Number of Unique Peptides,

• Spectral Counts

• Intensities for each protein. In cases where there are multiple values for a Protein-BioReplicate pair due to minute changes in sequence, the maximum value is taken for the pair. Any pairs without a value are assigned a value of NA.

Usage

artmsMsstatsSummary(
  evidence_file,
  prot_group_file,
  keys_file,
  results_file,
  return_df = FALSE,
  verbose = TRUE
)

Arguments

evidence_file	(char or data.frame) The filepath to the MaxQuant searched data (evidence) file (txt tab delimited file). Only works for the newer versions of the evidence file.
prot_group_file	(char) The filepath to the MaxQuant proteinGroups.txt file (txt tab delimited file) or data.frame
keys_file	(char) The filepath to the keys file used with MSStats (txt tab delimited file).
results_file	(char) The filepath to the MSStats results file in t he default long format (txt tab delimited file or data.frame).
return_df	(data.frame) Whether or not to return the results to the R environment upon completion. This is useful if this is being used in an R pipeline and you want to feed the results directly into the next stage of analysis via an R environment/terminal. Regardless, the results will be written to file. Default = FALSE
verbose	(logical) TRUE (default) shows function messages

Value

(data.frame or txt file) with the summary

Examples

# Testing warning if files are not submitted
test <- artmsMsstatsSummary(evidence_file = NULL,
                      prot_group_file = NULL,
                      keys_file = NULL,
                      results_file = NULL)

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