check_rii_proteomics: check proteomics reported ion intensity file

In MoTrPAC/MotrpacBicQC: QC/QA functions for the MoTrPAC community

check proteomics reported ion intensity file

Description

check whether the proteomics rri results files is following guidelines

Usage

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
}

MoTrPAC/MotrpacBicQC documentation built on Sept. 26, 2024, 11:10 a.m.