check proteomics reported ion intensity file — check_rii

check whether the proteomics rri results files is following guidelines

check_rii_proteomics(
  df_rri,
  isPTM,
  f_proof = TRUE,
  output_prefix = "rii-file",
  out_qc_folder = NULL,
  return_n_issues = FALSE,
  printPDF = TRUE,
  verbose = TRUE
)

Arguments

df_rri: (data.frame) proteomics rri data frame (required)
isPTM: (logical) TRUE if a PTM results file
f_proof: (logical) TRUE (default) to print out distribution and NA plots
output_prefix: (char) if f_proof = TRUE, provide a prefix for the output name
out_qc_folder: (char) if f_proof is TRUE, a folder path can be provided (otherwise print in current working directory)
return_n_issues: (logical) if TRUE returns the number of issues.
printPDF: (logical) if TRUE (default print plots to pdf)
verbose: (logical) TRUE (default) shows messages

Value

(int) number of issues identified

Examples

{
test <- check_rii_proteomics(df_rri = metadata_metabolites_named,
isPTM =  TRUE, return_n_issues = TRUE, verbose = FALSE)
# "test" should be NULL
}