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olink_qc.R
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olink_qc.R
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#' @title Check olink metadata proteins file
#'
#' @description check whether metadata-proteins.txt file is following guidelines
#' @param df (data.frame) metadata_proteins df
#' @param return_n_issues (logical) if `TRUE` returns the number of issues.
#' @param validate_uniprot (logical) if `TRUE`, check if all uniprot ids are valid
#' connecting to Uniprot. Note: depending on the number of ids, it might take
#' several finish to complete the validation
#' @param verbose (logical) `TRUE` (default) shows messages
#' @return (int) number of issues identified
#' @examples {
#' \dontrun{
#' check_metadata_proteins(df = metadata_proteins)
#' }
#' }
#' @export
check_metadata_proteins <- function(df,
return_n_issues = FALSE,
validate_uniprot = FALSE,
verbose = TRUE){
# issue_count
ic <- 0
df <- filter_required_columns(df = df,
type = "olproteins",
verbose = verbose)
# Evaluate every column
if( "olink_id" %in% colnames(df) ){
if( length(unique(df$olink_id)) != dim(df)[1] ){
duplis_details <- df$olink_id[duplicated(df$olink_id)]
duplis <- length(unique(duplis_details))
if(verbose) message(" - (-) `olink_id` non-unique values detected: ", duplis)
if(verbose) message("\t\t - ", paste(unique(duplis_details), collapse = "\n\t\t - "))
ic <- ic + 1
}else{
if(verbose) message(" + (+) `olink_id`: unique values: OK")
}
if( check_missing_values(df, "olink_id") ){
if(verbose) message(" - (-) `olink_id`: NA values detected: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `olink_id`: is missed: FAIL")
ic <- ic + 1
}
# uniprot_entry
if("uniprot_entry" %in% colnames(df)){
if( length(unique(df$uniprot_entry)) != dim(df)[1] ){
duplis_details <- df$uniprot_entry[duplicated(df$uniprot_entry)]
duplis <- length(unique(duplis_details))
if(verbose) message(" - ( ) `uniprot_entry` non-unique values detected (n duplications = ", duplis, "). This is OK")
if(verbose) message("\t\t - ", paste(unique(duplis_details), collapse = "\n\t\t - "))
}else{
if(verbose) message(" + (+) `uniprot_entry` unique values: OK")
}
if(validate_uniprot){
if(verbose) message(" + Validating every `uniprot_entry`. Connecting to Uniprot database (please, be patient as this step might take several minutes)")
all_true <- validate_uniprot_ids_with_uniprot(ids = unique(df$uniprot_entry))
if(all_true){
if(verbose) message(" + (+) `uniprot_entry` ids found in Uniprot database: OK")
} else{
if(verbose) message(" + (-) One or many `uniprot_entry` ids not found in Uniprot database: FAIL")
ic <- ic + 1
}
}
}else{
if(verbose) message(" - (-) `uniprot_entry` column missed: FAIL")
ic <- ic + 1
}
# assay
if("assay" %in% colnames(df)){
if(length(unique(df$assay)) != dim(df)[1]){
duplis_details <- df$assay[duplicated(df$assay)]
duplis <- length(unique(duplis_details))
if(verbose) message(" - ( ) `assay` non-unique values detected (n duplications = ", duplis, "). This is OK")
if(verbose) message("\t - ", paste(unique(duplis_details), collapse = "\n\t - "))
}else{
if(verbose) message(" + (+) `assay` unique values: OK")
}
if( check_missing_values(df, "assay") ){
if(verbose) message(" - (-) `assay` NA values detected: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `assay` column missed: FAIL")
ic <- ic + 1
}
if("missing_freq" %in% colnames(df)){
if( !all(is.numeric(df$missing_freq)) ){
if(verbose) message(" - (-) `missing_freq` non numeric values found: FAIL")
nonnum <- df$missing_freq[which(!grepl('^[0-9]', df$missing_freq))]
if(verbose) message("\n\t - ", paste(nonnum, collapse = "\n\t - "))
ic <- ic + 1
}else{
if(verbose) message(" + (+) `missing_freq` all numeric: OK")
}
if( check_missing_values(df, "missing_freq") ){
if(verbose) message(" - (-) `missing_freq` NA values detected: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `missing_freq` column missed: FAIL")
ic <- ic + 1
}
if("panel_name" %in% colnames(df)){
if(verbose){
message(" + (+) `panel_name` checking available panels:")
message("\t - ", paste(unique(df$panel_name), collapse = "\n\t - "))
}
if( check_missing_values(df, "panel_name") ){
if(verbose) message(" - (-) `panel_name` NA values detected: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `panel_name` column missed: FAIL")
ic <- ic + 1
}
if("panel_lot_nr" %in% colnames(df)){
if(verbose){
message(" + (+) `panel_lot_nr` checking available panels:")
message("\t - ", paste(unique(df$panel_lot_nr), collapse = "\n\t - "))
}
if( check_missing_values(df, "panel_lot_nr") ){
if(verbose) message(" - (-) `panel_lot_nr` NA values detected: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `panel_lot_nr` column missed: FAIL")
ic <- ic + 1
}
if("normalization" %in% colnames(df)){
if(verbose){
message(" + (+) `normalization` checking available panels:")
message("\t - ", paste(unique(df$normalization), collapse = "\n\t - "))
}
if( check_missing_values(df, "normalization") ){
if(verbose) message(" - (-) `normalization` NA values detected: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `normalization` column missed: FAIL")
ic <- ic + 1
}
if(return_n_issues) return(ic)
} #end check_metadata_proteins
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title check olink metadata samples file
#'
#' @description check whether metadata_sample is following guidelines
#' @param df (data.frame) olink metadata samples ata
#' @param return_n_issues (logical) if `TRUE` returns the number of issues.
#' @param verbose (logical) `TRUE` (default) shows messages
#' @return (int) number of issues identified
#' @examples {
#' \dontrun{
#' check_metadata_samples(df = metadata_sample_named)
#' }
#' }
#' @export
check_metadata_samples_olink <- function(df,
return_n_issues = FALSE,
verbose = TRUE){
olink_id = sample_order = unique_sample_order = plate_id = NULL
# issue_count
ic <- 0
# filter only expected columns
df <- filter_required_columns(df = df,
type = "olsamples",
verbose = verbose)
if( "sample_id" %in% colnames(df) ){
if( length(unique(df$sample_id)) != dim(df)[1] ){
if(verbose) message(" - (-) `sample_id`: Non-unique values detected: FAIL")
ic <- ic + 1
}else{
if(verbose) message(" + (+) `sample_id` seems OK")
}
}else{
if(verbose) message(" - (-) `sample_id` is missed: FAIL")
ic <- ic + 1
}
# sample_type: st
esample_types <- c("Sample", "QC-Pooled", "QC-Reference", "QC-Blank",
"QC-Identification", "QC-InternalStandard", "QC-PreRun",
"QC-ExternalStandard", "QC-DriftCorrection", "QC-ReCAS",
"QC-PlateControl")
if("sample_type" %in% colnames(df)){
if(!all(df$sample_type %in% esample_types)){
if(verbose) message(" - (-) Error: undefined sample types: ", appendLF = FALSE)
if(verbose) message("\n\t\t - ", paste(setdiff(df$sample_type, esample_types), collapse = "\n\t\t - "))
ic <- ic + 1
}else{
if(verbose) message(" + (+) `sample_type` seems OK")
}
}else{
if(verbose) message(" - (-) `sample_type` column missed: FAIL")
ic <- ic + 1
}
if( "plate_id" %in% colnames(df) ){
if(verbose) message(" + (+) `plate_id` is available: OK")
if( "sample_order" %in% colnames(df) ){
if(!all(is.numeric(df$sample_order))){
if(verbose) message(" - (-) `sample_order` non numeric values found: ", appendLF = FALSE)
nonnum <- df$sample_order[which(!grepl('^[0-9]', df$sample_order))]
if(verbose) message("\t\t - ", paste(nonnum, collapse = "\n\t\t - "))
ic <- ic + 1
}else{
if(verbose) message(" + (+) `sample_order` is numeric: OK")
# Check if the sample order is unique for each plate-id
non_unique_results <- df %>%
group_by(plate_id) %>%
summarise(unique_sample_order = all(length(unique(sample_order)) == length(sample_order))) %>%
filter(unique_sample_order == FALSE)
# Print plate_ids with non-unique sample_order values
if (nrow(non_unique_results) > 0) {
if(verbose) message(" - (-) `plate_id` with non-unique `sample_order` values: FAIL")
ic <- ic + 1
if(verbose) message("\t\t - ", paste(non_unique_results$plate_id, collapse = "\n\t\t - "))
} else {
if(verbose) message(" + (+) All `plate_id` values have unique `sample_order` values: OK\n")
}
}
}else{
if(verbose) message(" - (-) `sample_order` column missed: FAIL")
ic <- ic + 1
}
}else{
if(verbose) message(" - (-) `plate_id` column missed: FAIL")
ic <- ic + 1
}
if(return_n_issues) return(ic)
} #end check_metadata_sample_olink
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Check olink results
#'
#' @description check whether olink results file follows guidelines
#' @param df (data.frame) olink results data frame
#' @param return_n_issues (logical) if `TRUE` returns the number of issues.
#' @param verbose (logical) `TRUE` (default) shows messages
#' @return (int) number of issues identified
#' @examples {
#' \dontrun{
#' check_metadata_samples(df = olink_results)
#' }
#' }
#' @export
check_results_olink <- function(df,
return_n_issues = FALSE,
verbose = TRUE){
# issue_count
ic <- 0
is_empty_df <- ncol(df) == 0 && nrow(df) == 0
if(is_empty_df){
if(verbose) message(" - (-) `results` df is empty: FAIL")
if(return_n_issues){
ic <- 10
return(ic)
}else{
return("Data frame is empty")
}
}
if( "olink_id" %in% colnames(df) ){
if( length(unique(df$olink_id)) != dim(df)[1] ){
if(verbose) message(" - (-) `olink_id`: Non-unique values detected: FAIL")
ic <- ic + 1
}else{
if(verbose) message(" + (+) `olink_id` seems OK")
}
}else{
if(verbose) message(" - (-) `olink_id` is missed: FAIL")
ic <- ic + 1
}
# Get the names of all columns except "olink_id"
columns_to_check <- setdiff(names(df), "olink_id")
# Check if each of these columns is numeric
are_numeric <- sapply(df[columns_to_check], is.numeric)
# Print results
if( all(are_numeric) ) {
if(verbose) message(" + (+) All columns (except `olink_id`) are numeric: OK")
} else {
if(verbose) message(" - (-) `results.txt` contains non numeric columns: FAIL")
if(verbose) message("\t\t - ", paste(names(df[columns_to_check])[!are_numeric], collapse = "\n\t\t - "))
ic <- ic + 1
}
na_counts <- sapply(df[columns_to_check], function(column) sum(is.na(column)))
zero_counts <- sapply(df[columns_to_check], function(column) sum(column == 0))
# negative_counts <- sapply(df[columns_to_check], function(column) sum(column < 0))
total_na_count <- sum(na_counts)
total_zero_count <- sum(zero_counts)
# total_negative_count <- sum(negative_counts)
total_values_count <- sum(sapply(df[columns_to_check], length))
# Print the result
if(verbose){
message(paste0(" + ( ) Number of zeros in dataset: ", total_zero_count, " (out of ", total_values_count, " values)"))
message(paste0(" + ( ) Number of NAs in dataset: ", total_na_count, " (out of ", total_values_count, " values)"))
# if(total_negative_count > 0){
# message(paste0(" + (-) ", total_negative_count, " NEGATIVE VALUES IDENTIFIED: FAIL"))
# }
}
if(return_n_issues) return(ic)
} #end check_olink_results
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#' @title Cross-validate OLINK files
#'
#' @description Check values from results are vailable in both metdata proteins
#' and metadata samples files
#' @param r_o (data.frame) results df
#' @param m_s (char) metadata_sample df
#' @param m_p (char) metadata_proteins df
#' @param return_n_issues (logical) if `TRUE` returns the number of issues
#' @param verbose (logical) `TRUE` (default) shows messages
#' @return (int) number of issues identified
#' @examples {
#' \dontrun{
#' check_crossfile_olink_validation(r_o = results, m_s = metadata_samples, m_p = metadata_proteins)
#' }
#' }
#' @export
check_crossfile_olink_validation <- function(r_o,
m_s,
m_p,
return_n_issues = FALSE,
verbose = TRUE){
# issue_count
ic <- 0
# validate sample ids----
results_sampleids <- setdiff(names(r_o), "olink_id")
samples_sampleids <- unique(m_s$sample_id)
if( !setequal( results_sampleids, samples_sampleids ) ){
extra_in_results <- setdiff( results_sampleids, samples_sampleids )
if(length(extra_in_results) > 0){
if(verbose) message(" - (-) Samples in `results.txt` missed in `metadata-samples.txt`: FAIL")
if(verbose) message("\t\t - ", paste(extra_in_results, collapse = "\n\t\t - "))
}
extra_in_samples <- setdiff(results_sampleids, results_sampleids)
if(length(extra_in_samples)){
if(verbose) message(" - (-) Samples in `metadata-samples.txt` missed in `results.txt`: FAIL")
if(verbose) message("\t\t - ", paste(extra_in_samples, collapse = "\n\t\t - "))
}
ic <- ic + 1
}else{
if(verbose) message(" + (+) All samples in `results.txt` are available in `metadata-samples.txt`")
}
# validate olink_id----
results_olinkids <- r_o$olink_id
metaprt_olinkids <- m_p$olink_id
if( !setequal( results_olinkids, metaprt_olinkids ) ){
extra_in_results <- setdiff( results_sampleids, samples_sampleids )
if(length(extra_in_results > 0)){
if(verbose) message(" - (-) Column(s) NOT expected in `results.txt` file which are missed in `metadata-samples.txt`: \n\t\t - ",
paste(extra_in_results, collapse = "\n\t\t - "))
}
extra_in_msr <- setdiff(samples_sampleids, results_sampleids)
if(length(extra_in_msr)){
if(verbose) message(" - (-) Column(s) available in `metadata-samples.txt` missed in `results.txt`: \n\t\t - ",
paste(extra_in_msr, collapse = "\n\t\t - "))
}
ic <- ic + 1
}else{
if(verbose) message(" + (+) All `olink_id` from `results.txt` are available in `metadata-proteins.txt`")
}
if(return_n_issues) return(ic)
} # crossreference_olink_files
#' @title Load and Process Olink Batch Data
#'
#' @description
#' This function loads Olink batch data from the specified input directory.
#' It performs quality checks on the data and loads specific files related to
#' Olink data, including metadata for proteins and samples, and the results file.
#' It also integrates validation checks and warns if there are too many issues
#' identified in the data.
#'
#' @param input_results_folder A string representing the path to the folder
#' containing Olink batch data to be loaded and processed.
#' @param verbose Logical; if `TRUE`, prints detailed messages
#' during the loading process.
#'
#' @return A list containing data frames for metadata of proteins (m_p),
#' metadata of samples (m_s), and Olink results (r_o). If certain files
#' are not available, the corresponding entries in the list will be NULL.
#' @examples
#' \dontrun{
#' list_of_df <- load_olink_batch(input_results_folder = "/path/to/PROCESSED_YYYYMMDD/")
#' }
#' @export
load_olink_batch <- function(input_results_folder,
verbose = TRUE){
m_p = m_s = r_o = NULL
# Validations----
phase <- validate_phase(input_results_folder)
processfolder <- validate_processFolder(input_results_folder)
assay <- validate_assay(input_results_folder)
tissue_code <- validate_tissue(input_results_folder)
total_issues <- validate_olink(input_results_folder = input_results_folder,
cas = "broad_rg",
return_n_issues = TRUE,
verbose = verbose)
if(total_issues > 0){
message("\n\tWARNING!!! Too many issues identified (", total_issues,").
This batch should not be processed until the issues are solved")
}
vial_label <- NA
qc_samples <- NA
# Load olink----
if(verbose) message("# LOAD OLINK BATCH")
if(verbose) message("+ Site: Broad, Gerszten Lab")
if(verbose) message("+ Folder: `", paste0(input_results_folder),"`")
# qc metadata-proteins----
if(verbose) message("\n## QC `metadata_proteins`\n")
lista <- open_file(input_results_folder = input_results_folder,
filepattern = "metadata-proteins.txt",
verbose = verbose)
f_mp <- lista$flag
if(f_mp){
m_p_f <-lista$filename
m_p <- lista$df
}else{
if(verbose) message(" - (-) `metadata_proteins.txt` file not available")
ic_m_p <- 10
}
# qc metadata-samples------
if(verbose) message("\n## QC `metadata-samples.txt`\n")
lista <- open_file(input_results_folder = input_results_folder,
filepattern = "metadata-samples.txt",
verbose = verbose)
f_ms <- lista$flag
if(f_ms){
m_s_f <-lista$filename
m_s <- lista$df
}else{
if(verbose) message(" - (-) `metadata-samples.txt` file not available")
ic_m_s <- 10
}
# qc results olink------
if(verbose) message("\n## QC `results.txt`\n")
lista <- open_file(input_results_folder = input_results_folder,
filepattern = "results.txt",
verbose = verbose)
f_r <- lista$flag
if( f_r ){
r_o_f <-lista$filename
r_o <- lista$df
}else{
if(verbose) message(" - (-) `results.txt` file not available")
ic_r <- 10
}
# RETURN list of dfs-----
listdf <- list ("m_p" = m_p,
"m_s" = m_s,
"r_o" = r_o)
return(listdf)
}
#' Validate Olink Data
#'
#' This function validates Olink data based on a set of criteria, including
#' folder structure, metadata, and file contents. It supports optional
#' functionalities like creating a PDF report and DMAQC validation
#' (data only available at the BIC)
#'
#' @param input_results_folder A string representing the path to the folder
#' containing Olink results to be validated.
#' @param cas A character string indicating the CAS number.
#' @param return_n_issues Logical; if `TRUE`, the function returns the number of
#' detected issues.
#' @param full_report Logical; if `TRUE`, generates a full report of the
#' validation process.
#' @param f_proof Logical; if `TRUE`, generates proof plots for data validation.
#' @param printPDF Logical; if `TRUE` and `f_proof` is `TRUE`, saves the plots
#' to a PDF file, and in such case, then provide the desired path to output
#' the PDF file in the argument `out_qc_folder`
#' @param out_qc_folder Optional; a string specifying the path to the folder
#' where output PDF should be saved (only if `printPDF = TRUE`).
#' Default: current working directory
#' @param dmaqc_shipping_info (char) File path to the DMAQC file.
#' Only the BIC can use this argument
#' @param dmaqc_phase2validate (char) Provide phase to validate. This argument
#' is not required since it should be extracted from the input folder or from the
#' new required file `metadata_phase.txt`. Please, ignore.
#' However, if this argument is provided,
#' it will take priority and this will be the phase.
#' @param validate_uniprot Logical; if `TRUE`, validates against the UniProt
#' database.
#' @param verbose Logical; if `TRUE`, prints detailed messages during validation.
#'
#' @return Depending on the settings, this function may return the number of
#' issues found, generate reports or plots, or simply perform the
#' validation without returning anything.
#' @examples
#' \dontrun{
#' validate_olink("/path/to/results", cas = "broad_rg", return_n_issues = TRUE)
#' }
#' @export
validate_olink <- function(input_results_folder,
cas,
return_n_issues = FALSE,
full_report = FALSE,
f_proof = FALSE,
printPDF = FALSE,
out_qc_folder = NULL,
dmaqc_shipping_info = NULL,
dmaqc_phase2validate = FALSE,
validate_uniprot = FALSE,
verbose = TRUE){
olink_id = sample_order = plate_id = sample_id = NULL
# validate folder structure -----
validate_cas(cas = cas)
processfolder <- validate_processFolder(input_results_folder)
assay <- validate_assay(input_results_folder)
phase <- validate_phase(input_results_folder)
tissue_code <- validate_tissue(input_results_folder)
batch_folder <- validate_batch(input_results_folder)
# issue_count-----
ic <- 0
ic_m_p <- 0 # ic for metadata protein file
ic_m_s <- 0 # ic for metadata sample file
ic_r <- 0
ic_man <- 0 # required manifest f
if(is.null(dmaqc_shipping_info)){
ic_vl <- "missed"
} else{
ic_vl <- NA
}
vial_label <- NA
qc_samples <- NA
input_results_folder <- normalizePath(input_results_folder)
input_folder_short <- regmatches(input_results_folder, regexpr("(HUMAN|PASS).*RESULTS_[0-9]{8}", input_results_folder))
if(purrr::is_empty(input_folder_short)){
if(verbose) message("\nThe PROCESSED_YYYYMMDD folder full path is not correct. Example:")
if(verbose) message("/full/path/to/folder/HUMAN-PRECOVID/T02/BATCH1_20190822/RESULTS_20200302")
stop("Input folder not according to guidelines")
}
if(verbose) message("# OLINK QC report\n\n")
if(verbose) message("+ Site: ", cas)
if(verbose) message("+ Folder: `",paste0(input_folder_short),"`")
is_mp <- check_metadata_phase_file(input_results_folder = input_results_folder,
verbose = verbose)
if(!is_mp){
ic <- ic + 1
}
# Set phase-----
dmaqc_phase2validate <- set_phase(input_results_folder = input_results_folder,
dmaqc_phase2validate = dmaqc_phase2validate,
verbose = verbose)
phase2file <- generate_phase_details(phase_metadata = dmaqc_phase2validate)
# qc metadata-proteins----
if(verbose) message("\n## QC `metadata_proteins`\n")
lista <- open_file(input_results_folder = input_results_folder,
filepattern = "metadata-proteins.txt",
verbose = verbose)
f_mp <- lista$flag
if(f_mp){
m_p_f <-lista$filename
m_p <- lista$df
ic_m_p <- check_metadata_proteins(df = m_p,
return_n_issues = TRUE,
validate_uniprot = validate_uniprot,
verbose = verbose)
}else{
if(verbose) message(" - (-) `metadata_proteins.txt` file not available")
ic_m_p <- 10
}
# qc metadata-samples------
if(verbose) message("\n## QC `metadata-samples.txt`\n")
lista <- open_file(input_results_folder = input_results_folder,
filepattern = "metadata-samples.txt",
verbose = verbose)
f_ms <- lista$flag
if(f_ms){
m_s_f <-lista$filename
m_s <- lista$df
ic_m_s <- check_metadata_samples_olink(df = m_s,
return_n_issues = TRUE,
verbose = verbose)
# Extract the number of samples
if(!is.null(m_s)){
#Double check that the columns are there
if( all(c("sample_id", "sample_type") %in% colnames(m_s)) ){
vial_label <- length(m_s$sample_id[which(m_s$sample_type == "Sample")])
qc_samples <- length(m_s$sample_id[which(m_s$sample_type != "Sample")])
}
}
}else{
if(verbose) message(" - (-) `metadata-samples.txt` file not available")
ic_m_s <- 10
}
# qc results olink----
if(verbose) message("\n## QC `results.txt`\n")
lista <- open_file(input_results_folder = input_results_folder,
filepattern = "results.txt",
verbose = verbose)
f_r <- lista$flag
if( f_r ){
r_o_f <-lista$filename
r_o <- lista$df
ic_r <- check_results_olink(df = r_o,
return_n_issues = TRUE,
verbose = verbose)
}else{
if(verbose) message(" - (-) `results.txt` file not available")
ic_r <- 10
}
# qc cross validation-----
if(verbose) message("\n## Cross File Validation\n")
if(ic_m_p == 0 && ic_m_s == 0 && ic_r == 0) {
ic_c_f_v <- check_crossfile_olink_validation(r_o = r_o,
m_s = m_s,
m_p = m_p,
return_n_issues = TRUE,
verbose = verbose)
}else{
if(verbose) message(" - (-) File cross validation is not possible. PLease, fix issues affecting any of the files and run the validation again.")
}
# QC PLOTS------
if(f_proof){
if(verbose) message("\n\n## QC Plots\n")
output_prefix <- paste0(cas, ".", tolower(phase2file), ".", tissue_code, ".",tolower(assay), ".", tolower(processfolder))
output_prefix <- gsub("\\|", "_", output_prefix)
if(f_r & f_ms & f_mp){
# Ensure there are enough compounds to generate plots
if( dim(r_o)[1] > 1 ){
results_long <- r_o %>% tidyr::pivot_longer(cols = -c(olink_id),
names_to = "sample_id",
values_to = "value")
results_long <- merge(m_s, results_long, by = c("sample_id"))
results_long$sample_id <- as.character(results_long$sample_id)
results_long$sample_id <- as.factor(results_long$sample_id)
results_long$sample_type <- as.factor(results_long$sample_type)
results_long <- results_long[which(results_long$value != 0),]
results_long <- results_long[!is.na(results_long$value),]
# sort by plate_id and sample_order
results_long <- results_long %>%
arrange(plate_id, sample_order) %>%
mutate(sample_id_ordered = factor(sample_id, levels = unique(sample_id)))
r_p <- merge(m_p, r_o, by = "olink_id")
plot_basic_olink_qc(results = r_p,
results_long = results_long,
out_qc_folder = out_qc_folder,
output_prefix = output_prefix,
printPDF = printPDF,
verbose = verbose)
}else{
message(" (-) QC plots are not possible: not enough compounds")
}
}else{
if(verbose) message("\n- (-) QC plots are not possible: critical datasets are missed")
}
} # qc plots
# MANIFEST file-----
if(verbose) message("\n## QC `file_manifest_YYYYMMDD.csv` (required)\n")
batch <- gsub("(.*)(RESULTS.*)", "\\1", input_results_folder)
file_manifest <- list.files(normalizePath(batch),
pattern="file_manifest.*csv",
ignore.case = TRUE,
full.names=TRUE,
recursive = TRUE)
if(length(file_manifest) == 0){
f_man <- FALSE
if(verbose) message(" - (-) `file_manifest_YYYYMMDD.csv` file not available")
ic <- ic + 1
}else if(length(file_manifest) >= 1){
first_manifest <- sort(basename(file_manifest), decreasing = TRUE)[1]
file_manifest <- file_manifest[grep(first_manifest, file_manifest)]
f_man <- TRUE
}
if(f_man){
manifest <- read.csv(file_manifest)
mani_columns <- c("file_name", "md5")
if( all( mani_columns %in% colnames(manifest)) ){
if(verbose) message(" + (+) `file_name, md5` columns available in manifest file")
# Replace windows based backlash
if(any(grepl("\\\\", manifest$file_name))){
manifest$file_name <- gsub("\\\\", "/", manifest$file_name)
}
manifest$file_base <- basename(manifest$file_name)
if(f_mp){
metadata_proteins_file <- basename(manifest$file_name[grepl("metadata-proteins", manifest$file_name)])[1]
tocheck <- basename(m_p_f)
if(!is.na(metadata_proteins_file)){
if( tocheck == metadata_proteins_file){
if(verbose) message(" + (+) `metadata-proteins` file included in manifest: OK")
}else{
if(verbose) message(" - (-) `metadata-proteins` file is not included in manifest file: FAIL")
ic_man <- ic_man + 1
}
}else{
if(verbose) message(" - (-) `metadata-proteins` file is not included in manifest file: FAIL")
ic_man <- ic_man + 1
}
}
if(f_ms){
metadata_samples_file <- basename(manifest$file_name[grepl("metadata-samples", manifest$file_name)])[1]
tocheck <- basename(m_s_f)
if(!is.na(metadata_samples_file)){
if( tocheck == metadata_samples_file ){
if(verbose) message(" + (+) `metadata-samples` file included in manifest: OK")
}else{
if(verbose) message(" - (-) `metadata-samples` file is not included in manifest file: FAIL")
ic_man <- ic_man + 1
}
}else{
if(verbose) message(" - (-) `metadata-samples` file is not included in manifest file: FAIL")
ic_man <- ic_man + 1
}
} # f_msn
if(f_r){
results_file <- basename(manifest$file_name[grepl("results", manifest$file_name)])[1]
tocheck <- basename(r_o_f)
if(!is.na(results_file)){
if( tocheck == results_file ){
if(verbose) message(" + (+) `results` file included in manifest: OK")
}else{
if(verbose) message(" - (-) `results` file is not included in manifest file: FAIL")
ic_man <- ic_man + 1
}
}
}
if( any(is.na(manifest$md5)) ){
if(verbose) message(" - (-) MD5 column contains NA values: FAIL")
ic_man <- ic_man + 1
}
}else{
if(verbose) message(" - (-) Not all the required columns are available: FAIL")
ic_man <- ic_man + 1
}
}else{
if(verbose) message(" - (-) MANIFEST (REQUIRED) FILE NOT FOUND (`file_manifest_DATE.txt`). Please, check guidelines")
ic_man <- ic_man + 6
ic <- ic + 1
} # QC manifest
# DMAQC validation -----
if(verbose) message("\n\n## DMAQC validation\n")
failed_samples <- check_failedsamples(input_results_folder = input_results_folder,
verbose = verbose)
# Validate vial labels from DMAQC
if( is.na(ic_vl) ){
if(f_ms){
vl_results <- m_s$sample_id[which(m_s$sample_type == "Sample")]
outfile_missed_viallabels <- paste0(cas, ".", tolower(phase2file), ".", tissue_code, ".",tolower(assay), ".", tolower(processfolder))
outfile_missed_viallabels <- gsub("\\|", "_", outfile_missed_viallabels)
ic_vl <- check_viallabel_dmaqc(vl_submitted = vl_results,
tissue_code = tissue_code,
cas = cas,
phase = dmaqc_phase2validate,
failed_samples = failed_samples,
dmaqc_shipping_info = dmaqc_shipping_info,
out_qc_folder = out_qc_folder,
outfile_missed_viallabels = outfile_missed_viallabels,
return_n_issues = TRUE,
verbose = verbose)
}
}
# RETURN report-----
if(ic > 4){
message("\nTOTAL NUMBER OF CRITICAL ERROR: ", ic,"\n")
message("WARNING: Too many errors. Revise input folder")
}
batchversion <- stringr::str_extract(string = input_results_folder, pattern = "BATCH.*_[0-9]+/RESULTS_[0-9]+")
qc_date <- Sys.time()
qc_date <- gsub("-", "", qc_date)
qc_date <- gsub(" ", "_", qc_date)
qc_date <- gsub(":", "", qc_date)
t_name <- bic_animal_tissue_code$bic_tissue_name[which(bic_animal_tissue_code$bic_tissue_code == tissue_code)]
if(return_n_issues){
total_issues <- sum(ic, ic_man, ic_m_p, ic_m_s, ic_r, na.rm = TRUE)
if(verbose) message("\nTOTAL NUMBER OF ISSUES: ", total_issues,"\n")
if(full_report){
reports <- data.frame(cas = cas,
phase = dmaqc_phase2validate,
tissue = tissue_code,
t_name = t_name,
assay = assay,
version = batchversion,
vial_label = vial_label,
qc_samples = qc_samples,
dmaqc_valid = ic_vl,
critical_issues = ic,
manifest = ic_man,
m_prot = ic_m_p,
m_sample = ic_m_s,
results = ic_r,
qc_date = qc_date)
return(reports)
}else{
return(total_issues)
}
}
} # Validate OLINK
#' @title Write olink data release
#'
#' @description Write out olink data releases. Doesn't check whether
#' data has been submited according to guidelines
#' @param input_results_folder (char) Path to the RESULTS_YYYYMMDD folder
#' @param folder_name (char) output folder name.
#' @param folder_root (char) absolute path to write the output folder.
#' Default: current directory
#' @param version_file (char) file version number (v#.#)
#' @param verbose (logical) `TRUE` (default) shows messages
#' @return bic release folder/file structure
#' `PHASE/OMICS/TCODE_NAME/ASSAY/` and file names, including:
#' - `motrpac_phase-code_tissuecode_assay_file-details-version.txt`
#' where files-details can be:
#' - `metadata-proteins`,
#' - `metadata-samples`,
#' - `results`
#' @examples
#' \dontrun{
#' write_olink_releases(
#' input_results_folder = "/full/path/to/RESULTS_YYYYMMDD/")
#' }
#' @export
write_olink_releases <- function(input_results_folder,
folder_name = "motrpac_release",
folder_root = NULL,
version_file = "v1.0",
verbose = TRUE){
# Get names from input_results_folder------
assay <- validate_assay(input_results_folder)
phase <- validate_phase(input_results_folder)
phase_metadata <- set_phase(input_results_folder = input_results_folder,
dmaqc_phase2validate = FALSE,
verbose = FALSE)
phase_details <- generate_phase_details(phase_metadata)
tissue_code <- validate_tissue(input_results_folder)
folder_tissue <- bic_animal_tissue_code$tissue_name_release[which(bic_animal_tissue_code$bic_tissue_code == tissue_code)]
# # or make a function:
# get_folder_tissue <- function(tissue_code) {
# folder_tissue <- MotrpacBicQC::bic_animal_tissue_code$tissue_name_release[
# which(MotrpacBicQC::bic_animal_tissue_code$bic_tissue_code == tissue_code)
# ]
# return(folder_tissue)
# }
#
# folder_tissue2 <- get_folder_tissue(tissue_code)
if( length(assay_codes$assay_code[which(assay_codes$submission_code == assay)]) == 1 ){
folder_assay <- assay_codes$assay_code[which(assay_codes$submission_code == assay)]
}else{
stop("ASSAY code ", assay, " not available in `assay_codes`")
}
if(verbose) message("+ Writing out: ", phase_details, " ", tissue_code, " ", assay, " files", appendLF = FALSE)
# Load olink datasets----
olink_df <- load_olink_batch(input_results_folder = input_results_folder,
verbose = FALSE)
# Create output folder-------
if (is.null(folder_root)){