artmsMsstatsSummary: Summarize the MSStats results and data quantification

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

Summarize the MSStats results and data quantification

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)

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