Outputs the spectral counts from the MaxQuant evidence file.

Source: R/MSstats_functions.R

Outputs the spectral counts from the MaxQuant evidence file.

artmsSpectralCounts(
  evidence_file,
  keys_file,
  output_file = NULL,
  verbose = TRUE
)

Arguments

evidence_file

(char) Maxquant evidence file or data object
keys_file

(char) Keys file with the experimental design or data object
output_file

(char) Output file name (add .txt extension). If NULL (default) it returns a data.frame object
verbose

(logical) TRUE (default) shows function messages

Value

A txt file with biological replicates, protein id, and spectral count columns

Examples

summary_spectral_counts <- artmsSpectralCounts(
                                 evidence_file = artms_data_ph_evidence,
                                 keys_file = artms_data_ph_keys)

#> >> EXTRACTING SPECTRAL COUNTS FROM THE EVIDENCE FILE 
#> >> MERGING FILES