From 6f5960af5227698f928895d5d883c67f8cf9e180 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 22 Mar 2024 18:24:05 -0700 Subject: [PATCH 1/7] enchance validate_refmetname: ensure checking the refmet standarized name #233 --- R/metabolomics_data_dictionary.R | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/R/metabolomics_data_dictionary.R b/R/metabolomics_data_dictionary.R index 907d4b77..41e83832 100644 --- a/R/metabolomics_data_dictionary.R +++ b/R/metabolomics_data_dictionary.R @@ -77,7 +77,6 @@ get_and_validate_mdd <- function(remove_duplications = FALSE){ validate_refmetname <- function(dataf, verbose){ irm <- 0 - idna <- 0 for(i in 1:dim(dataf)[1]){ rn <- dataf$refmet_name[i] @@ -100,11 +99,15 @@ validate_refmetname <- function(dataf, verbose){ if(here$refmet_name == "-"){ if(verbose) message(paste0(" (-) `refmet_name` [`", rn, "`] not available in RefMet. Please, contact MW/BIC (Error RN1)")) irm <- irm + 1 - idna <- idna + 1 + }else{ + if(here$refmet_name != rn){ + if(verbose) message(paste0(" (-) `refmet_name` [`", rn, "`] must be modified to the RefMet Standarized name: \"", here$refmet_name, "\" (Error RN2)")) + irm <- irm + 1 + } } } - if(idna > 0){ - if(verbose) message(" (-) Total number of missed ids on MW: ", idna) + if(irm > 0){ + if(verbose) message(" (-) Total number of missed ids on MW: ", irm) } return(irm) } From 39f4ee8c82a48669fda5176b5e1bf9e71d7a0b13 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 22 Mar 2024 18:24:18 -0700 Subject: [PATCH 2/7] Update refmet tests #233 --- tests/testthat/test-metabolomics_qc.R | 2 +- tests/testthat/test-refmet.R | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/tests/testthat/test-metabolomics_qc.R b/tests/testthat/test-metabolomics_qc.R index bd85ce24..79cbbeeb 100644 --- a/tests/testthat/test-metabolomics_qc.R +++ b/tests/testthat/test-metabolomics_qc.R @@ -1,7 +1,7 @@ context("Test check_metabolomics functions") test_that("check_metadata_metabolites returns the right number of issues", { - expect_equal(check_metadata_metabolites(df = metadata_metabolites_named, name_id = "named", return_n_issues = TRUE, verbose = FALSE), 0) + expect_equal(check_metadata_metabolites(df = metadata_metabolites_named, name_id = "named", return_n_issues = TRUE, verbose = TRUE), 1) expect_equal(check_metadata_metabolites(df = metadata_metabolites_unnamed, name_id = "unnamed", return_n_issues = TRUE, verbose = FALSE), 0) expect_equal(check_metadata_metabolites(df = metadata_metabolites_unnamed, name_id = "named", return_n_issues = TRUE, verbose = FALSE), 2) }) diff --git a/tests/testthat/test-refmet.R b/tests/testthat/test-refmet.R index 017a05c1..c43d2693 100644 --- a/tests/testthat/test-refmet.R +++ b/tests/testthat/test-refmet.R @@ -14,6 +14,22 @@ test_that("validate_refmetname handles known refmet_name correctly", { expect_equal(actual_missed_ids, 3) }) +test_that("validate_refmetname to very similar refmet_names", { + # Example test data + # https://www.metabolomicsworkbench.org/rest/refmet/match/2-Amino-6-hydroxyhexanoic acid/name/ + # https://www.metabolomicsworkbench.org/rest/refmet/match/2-amino-6-hydroxyhexanoic acid/name/ + test_data <- data.frame( + refmet_name = c("2-Amino-6-hydroxyhexanoic acid", "2-amino-6-hydroxyhexanoic acid", "2-Aamino-6-hydroxyhexanoic acid", "-"), + stringsAsFactors = FALSE + ) + + # Call the function with verbose = FALSE to suppress messages during test + actual_missed_ids <- validate_refmetname(test_data, verbose = TRUE) + + # Check if the actual missed IDs match the expected outcome + expect_equal(actual_missed_ids, 3) +}) + test_that("Successful API call returns correctly structured list with no additional elements", { # Known good refmet_name that will return a successful response From 122d65ddbceef661b5e652657d289050716474b0 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 22 Mar 2024 18:50:26 -0700 Subject: [PATCH 3/7] open_file: accept only tab delimited files #234 --- R/misc.R | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/R/misc.R b/R/misc.R index 25bdef18..ca1565df 100644 --- a/R/misc.R +++ b/R/misc.R @@ -346,12 +346,18 @@ open_file <- function(input_results_folder, ofile <- NULL filename <- NULL }else{ - flag <- TRUE + filename <- file_metametabolites[1] - ofile <- read.delim(filename, stringsAsFactors = FALSE, check.names = FALSE) - ofile <- remove_empty_columns(ofile, verbose = verbose) - ofile <- remove_empty_rows(ofile, verbose = verbose) - if(verbose) message(" + (+) File successfully opened") + file_ext <- sub(".*\\.(.*)$", "\\1", filename) + if (!file_ext %in% c("txt", "tsv")) { + if(verbose) message(" - (-) File extension must be .txt or .tsv (only tab delimited files accepted): FAIL") + }else{ + ofile <- read.delim(filename, stringsAsFactors = FALSE, check.names = FALSE) + ofile <- remove_empty_columns(ofile, verbose = verbose) + ofile <- remove_empty_rows(ofile, verbose = verbose) + if(verbose) message(" + (+) File successfully opened") + flag <- TRUE + } } if(flag){ From 0eef09e02621f04a81d905ecb6c101590fc4f306 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 22 Mar 2024 19:00:56 -0700 Subject: [PATCH 4/7] enhance: dl_read_gcp: replace data table by read_delim #232 #227 --- R/misc.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/R/misc.R b/R/misc.R index ca1565df..7ddad5ef 100644 --- a/R/misc.R +++ b/R/misc.R @@ -14,7 +14,7 @@ #' @import naniar #' @import progress #' @import purrr -#' @importFrom readr read_lines +#' @importFrom readr read_lines read_delim #' @importFrom scales percent #' @importFrom stats median reorder #' @import stringr @@ -136,8 +136,9 @@ dl_read_gcp <- function(path, } # read in the data as a data.table if(file.exists(new_path)){ - dt <- data.table::fread(new_path, sep=sep, header=header,...) - return(dt) + df <- readr::read_delim(new_path, delim = sep, col_names = header, skip_empty_rows = TRUE, show_col_types = FALSE, ...) + df <- as.data.frame(df) + return(df) }else{ stop("- Problems loading the file. Possible reason: the file does not exist in the bucket anymore. Please, validate the address. Re-run this command again with `verbose = TRUE`)") } From 17fea70b350357af5c5425aac344426e255cc4e1 Mon Sep 17 00:00:00 2001 From: David JM Date: Fri, 22 Mar 2024 19:21:18 -0700 Subject: [PATCH 5/7] enhance: only one metadata_phase file allowed #224 --- NAMESPACE | 1 + R/misc.R | 6 +++++- R/validations.R | 7 ++++++- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index cf3c48c6..e54ff2bd 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -76,6 +76,7 @@ importFrom(httr,status_code) importFrom(inspectdf,inspect_na) importFrom(jsonlite,fromJSON) importFrom(lubridate,parse_date_time) +importFrom(readr,read_delim) importFrom(readr,read_lines) importFrom(scales,percent) importFrom(stats,median) diff --git a/R/misc.R b/R/misc.R index 7ddad5ef..fede7ff2 100644 --- a/R/misc.R +++ b/R/misc.R @@ -455,10 +455,14 @@ set_phase <- function(input_results_folder, ignore.case = TRUE, full.names=TRUE, recursive = TRUE) + + if(length(file_phase) > 1){ + if(verbose) message("- (-) `More than one `metadata_phase.txt` file available. Only one is valid (place the valid one in the BATCH folder): FAIL") + } # To be adjusted if two different batches are provided: if ( !(purrr::is_empty(file_phase)) ){ - phase_details <- readr::read_lines(file_phase, n_max = 1) + phase_details <- readr::read_lines(file_phase[1], n_max = 1) if ( !(is.na(phase_details) || phase_details == '') ){ if(verbose) message("+ Motrpac phase reported: ", phase_details, " (info from metadata_phase.txt available): OK") diff --git a/R/validations.R b/R/validations.R index a0524ff0..bfe9335b 100644 --- a/R/validations.R +++ b/R/validations.R @@ -78,7 +78,12 @@ check_metadata_phase_file <- function(input_results_folder, if(verbose) message("- (-) `BATCH#_YYYYMMDD/metadata_phase.txt` file does not exist: FAIL") return(FALSE) }else{ - return(TRUE) + if(length(file_phase) > 1){ + if(verbose) message("- (-) `More than one `metadata_phase.txt` file available. Only one is valid (place the valid one in the BATCH folder): FAIL") + return(FALSE) + }else{ + return(TRUE) + } } } From 7e74d8faae2836a2d3d78c31c4de659ca072898a Mon Sep 17 00:00:00 2001 From: David JM Date: Mon, 25 Mar 2024 11:14:59 -0700 Subject: [PATCH 6/7] Update get_and_validate_mdd - Update REST service url - Update Documentation - Remove dependency on data.table #231 --- R/metabolomics_data_dictionary.R | 88 +++++++++++++++++++------------- man/get_and_validate_mdd.Rd | 48 ++++++++++++++--- 2 files changed, 94 insertions(+), 42 deletions(-) diff --git a/R/metabolomics_data_dictionary.R b/R/metabolomics_data_dictionary.R index 41e83832..0a5ccab6 100644 --- a/R/metabolomics_data_dictionary.R +++ b/R/metabolomics_data_dictionary.R @@ -1,44 +1,61 @@ # All about the RefMet data dictionary - -#' @title Get and validate the entire RefMet database from Metabolomics Workbench +#' @title Get and Validate the Entire RefMet Database from Metabolomics Workbench +#' +#' @description This function fetches and validates the Metabolomics Data Dictionary +#' from the Metabolomics Workbench. It provides options to remove duplicates. +#' +#' @param remove_duplications Logical; if `TRUE`, removes duplicate entries based on +#' the `refmet_name` column. +#' @param verbose Logical; if `TRUE` (default), displays progress messages and warnings +#' during the function execution. +#' +#' @return Returns a data frame with the following columns: +#' \describe{ +#' \item{\code{refmet_name}}{Character; the name standarized refmet name} +#' \item{\code{pubchem_cid}}{Character; the PubChem compound ID.} +#' \item{\code{lm_id}}{Character; the LIPID MAPS ID.} +#' \item{\code{inchi_key}}{Character; the International Chemical Identifier Key.} +#' \item{\code{exactmass}}{Numeric; the exact mass of the metabolite.} +#' \item{\code{formula}}{Character; the chemical formula of the metabolite.} +#' \item{\code{super_class}}{Character; the superclass category of the metabolite.} +#' \item{\code{main_class}}{Character; the main class category of the metabolite.} +#' \item{\code{sub_class}}{Character; the subclass category of the metabolite.} +#' \item{\code{hmdb_id}}{Character; the Human Metabolome Database ID.} +#' \item{\code{kegg_id}}{Character; the Kyoto Encyclopedia of Genes and Genomes ID.} +#' } +#' Each row of the data frame represents a unique metabolite entry from the +#' Metabolomics Workbench Data Dictionary. +#' +#' @details This function downloads the entire RefMet database from the Metabolomics +#' Workbench using their REST API. The data is initially fetched in JSON format and +#' then converted to a data frame. The function checks for the presence of a 'name' +#' column in the data frame, renaming it to 'refmet_name' for consistency. It also +#' provides an option to remove duplicate entries based on the 'refmet_name' column. +#' If duplicates are found and \code{remove_duplications} is `FALSE`, the function will +#' list the duplicated IDs but will not remove them. This can be helpful for reviewing +#' the data quality and consistency. +#' +#' @examples +#' \dontrun{ +#' refmet <- get_and_validate_mdd(remove_duplications = TRUE, verbose = TRUE) +#' head(refmet) +#' } #' -#' @description Get and validate Metabolomics Data Dictionary from -#' Metabolomics Workbench -#' @param remove_duplications (logical) if `TRUE``, removes duplications. -#' @return (vector) PHASE code #' @export +get_and_validate_mdd <- function(remove_duplications = FALSE, verbose = TRUE){ -# get_and_validate_mdd <- function(remove_duplications = FALSE){ -# -# refmet <- MotrpacBicQC::metabolomics_data_dictionary -# -# if(remove_duplications){ -# # REMOVE DUPLICATIONS -# if( any(duplicated(refmet$refmet_name)) ){ -# duplirefmets <- length(refmet$refmet_name[(duplicated(refmet$refmet_name))]) -# # message("WARNING: [ ",duplirefmets, " ] DUPLICATION(s) found in data dictionary!") -# refmet <- refmet[!(duplicated(refmet$refmet_name)),] -# } -# } -# return(refmet) -# } - -get_and_validate_mdd <- function(remove_duplications = FALSE){ - - .id = name = NULL + name = NULL + if(verbose) message("- Warning: Downloading data from Metabolomics Workbench. This might take a few minutes.") # REST metabolomics workbench data dictionary - # Previous REST version (motrpac only) + # Previous REST versions # refmetjson <- jsonlite::fromJSON("https://www.metabolomicsworkbench.org/rest/refmet/motrpac") - refmetjson <- jsonlite::fromJSON("https://www.metabolomicsworkbench.org/rest/refmet/all/") - - dt_list <- purrr::map(refmetjson, as.data.table) - dt <- data.table::rbindlist(dt_list, fill = TRUE, idcol = T) - df <- as.data.frame(dt) - - colnames(df) <- tolower(colnames(df)) + # refmetjson <- jsonlite::fromJSON("https://www.metabolomicsworkbench.org/rest/refmet/all/") + refmetjson <- jsonlite::fromJSON("https://www.metabolomicsworkbench.org/rest/refmet/all_ids/") + + df <- purrr::map_dfr(refmetjson, ~ as.data.frame(.x), .id = "id") if( !("name" %in% colnames(df)) ){ stop("`refmet_name` column not found in the Metabolomics Workbench data dictionary") @@ -49,12 +66,11 @@ get_and_validate_mdd <- function(remove_duplications = FALSE){ # CHECK DUPLICATIONS if(any(duplicated(df$refmet_name))){ duplications <- df[duplicated(df$refmet_name),] - message("Duplicated ids: ", length(duplications$refmet_name)) - message("IDS: ", paste(duplications$refmet_name, collapse = ", ")) - message("DUPLICATIONS IN REFMET ONLINE (REST VERSION)") + if(verbose) message("Duplicated ids: ", length(duplications$refmet_name)) + if(verbose) message("IDS: ", paste(duplications$refmet_name, collapse = ", ")) } - refmet <- subset(df, select = -c(.id)) + refmet <- subset(df, select = -c(id)) if(remove_duplications){ # REMOVE DUPLICATIONS diff --git a/man/get_and_validate_mdd.Rd b/man/get_and_validate_mdd.Rd index 3385f637..a204c289 100644 --- a/man/get_and_validate_mdd.Rd +++ b/man/get_and_validate_mdd.Rd @@ -2,17 +2,53 @@ % Please edit documentation in R/metabolomics_data_dictionary.R \name{get_and_validate_mdd} \alias{get_and_validate_mdd} -\title{Get and validate the entire RefMet database from Metabolomics Workbench} +\title{Get and Validate the Entire RefMet Database from Metabolomics Workbench} \usage{ -get_and_validate_mdd(remove_duplications = FALSE) +get_and_validate_mdd(remove_duplications = FALSE, verbose = TRUE) } \arguments{ -\item{remove_duplications}{(logical) if `TRUE``, removes duplications.} +\item{remove_duplications}{Logical; if \code{TRUE}, removes duplicate entries based on +the \code{refmet_name} column.} + +\item{verbose}{Logical; if \code{TRUE} (default), displays progress messages and warnings +during the function execution.} } \value{ -(vector) PHASE code +Returns a data frame with the following columns: +\describe{ +\item{\code{refmet_name}}{Character; the name standarized refmet name} +\item{\code{pubchem_cid}}{Character; the PubChem compound ID.} +\item{\code{lm_id}}{Character; the LIPID MAPS ID.} +\item{\code{inchi_key}}{Character; the International Chemical Identifier Key.} +\item{\code{exactmass}}{Numeric; the exact mass of the metabolite.} +\item{\code{formula}}{Character; the chemical formula of the metabolite.} +\item{\code{super_class}}{Character; the superclass category of the metabolite.} +\item{\code{main_class}}{Character; the main class category of the metabolite.} +\item{\code{sub_class}}{Character; the subclass category of the metabolite.} +\item{\code{hmdb_id}}{Character; the Human Metabolome Database ID.} +\item{\code{kegg_id}}{Character; the Kyoto Encyclopedia of Genes and Genomes ID.} +} +Each row of the data frame represents a unique metabolite entry from the +Metabolomics Workbench Data Dictionary. } \description{ -Get and validate Metabolomics Data Dictionary from -Metabolomics Workbench +This function fetches and validates the Metabolomics Data Dictionary +from the Metabolomics Workbench. It provides options to remove duplicates. +} +\details{ +This function downloads the entire RefMet database from the Metabolomics +Workbench using their REST API. The data is initially fetched in JSON format and +then converted to a data frame. The function checks for the presence of a 'name' +column in the data frame, renaming it to 'refmet_name' for consistency. It also +provides an option to remove duplicate entries based on the 'refmet_name' column. +If duplicates are found and \code{remove_duplications} is \code{FALSE}, the function will +list the duplicated IDs but will not remove them. This can be helpful for reviewing +the data quality and consistency. +} +\examples{ +\dontrun{ + refmet <- get_and_validate_mdd(remove_duplications = TRUE, verbose = TRUE) + head(refmet) +} + } From f523ef1672f30047453e96a267025481ca128e61 Mon Sep 17 00:00:00 2001 From: David JM Date: Mon, 25 Mar 2024 14:20:55 -0700 Subject: [PATCH 7/7] MotrpacBicQC 0.9.3: critical update of refmet name additional validation --- DESCRIPTION | 4 +- NEWS.md | 12 +++ docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/articles/other_functions.html | 4 +- docs/articles/qc_metabolomics.html | 10 ++- docs/articles/qc_olink.html | 4 +- docs/articles/qc_proteomics.html | 4 +- docs/authors.html | 6 +- docs/index.html | 2 +- docs/news/index.html | 14 +++- docs/notes_developers.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/assay_abbr.html | 2 +- docs/reference/assay_codes.html | 2 +- docs/reference/assay_order.html | 2 +- docs/reference/bic_animal_tissue_code.html | 2 +- .../check_crossfile_olink_validation.html | 2 +- docs/reference/check_failedsamples.html | 2 +- docs/reference/check_manifest_rawdata.html | 2 +- .../reference/check_metadata_metabolites.html | 8 +- docs/reference/check_metadata_phase_file.html | 2 +- docs/reference/check_metadata_proteins.html | 2 +- docs/reference/check_metadata_samples.html | 2 +- .../check_metadata_samples_olink.html | 2 +- docs/reference/check_missing_values.html | 2 +- docs/reference/check_ratio_proteomics.html | 2 +- docs/reference/check_results.html | 2 +- docs/reference/check_results_olink.html | 2 +- docs/reference/check_rii_proteomics.html | 2 +- .../check_vial_metadata_proteomics.html | 2 +- docs/reference/check_viallabel_dmaqc.html | 2 +- .../reference/combine_metabolomics_batch.html | 2 +- docs/reference/create_folder.html | 2 +- docs/reference/dl_read_gcp.html | 2 +- docs/reference/filter_required_columns.html | 2 +- docs/reference/generate_phase_details.html | 2 +- docs/reference/get_and_validate_mdd.html | 79 ++++++++++++++++--- docs/reference/get_full_path2batch.html | 2 +- docs/reference/group_abbr.html | 2 +- docs/reference/group_cols.html | 2 +- docs/reference/index.html | 4 +- docs/reference/load_metabolomics_batch.html | 2 +- docs/reference/load_olink_batch.html | 2 +- docs/reference/load_proteomics.html | 2 +- docs/reference/merge_all_metabolomics.html | 2 +- .../merge_metabolomics_metadata.html | 2 +- .../merge_phenotype_metabolomics.html | 2 +- .../metabolomics_data_dictionary.html | 2 +- .../reference/metadata_metabolites_named.html | 2 +- .../metadata_metabolites_unnamed.html | 2 +- docs/reference/metadata_sample_named.html | 2 +- docs/reference/metadata_sample_unnamed.html | 2 +- docs/reference/open_file.html | 2 +- docs/reference/phenotypes_pass1a06_short.html | 2 +- .../reference/plot_basic_metabolomics_qc.html | 2 +- docs/reference/plot_basic_olink_qc.html | 2 +- docs/reference/proteomics_plots_rii.html | 2 +- docs/reference/remove_empty_columns.html | 2 +- docs/reference/remove_empty_rows.html | 2 +- docs/reference/results_named.html | 2 +- docs/reference/results_unnamed.html | 2 +- docs/reference/set_phase.html | 2 +- docs/reference/sex_abbr.html | 2 +- docs/reference/sex_cols.html | 2 +- docs/reference/tissue_abbr.html | 2 +- docs/reference/tissue_cols.html | 2 +- docs/reference/tissue_order.html | 2 +- docs/reference/validate_assay.html | 2 +- docs/reference/validate_batch.html | 2 +- docs/reference/validate_cas.html | 2 +- docs/reference/validate_dates_times.html | 2 +- docs/reference/validate_lc_column_id.html | 2 +- docs/reference/validate_metabolomics.html | 2 +- docs/reference/validate_na_empty.html | 2 +- docs/reference/validate_olink.html | 2 +- docs/reference/validate_phase.html | 2 +- docs/reference/validate_processFolder.html | 2 +- docs/reference/validate_proteomics.html | 2 +- docs/reference/validate_refmetname.html | 2 +- docs/reference/validate_tissue.html | 2 +- docs/reference/validate_two_phases.html | 2 +- .../validate_uniprot_ids_with_uniprot.html | 2 +- docs/reference/validate_yyyymmdd_dates.html | 2 +- .../write_metabolomics_releases.html | 2 +- docs/reference/write_olink_releases.html | 2 +- docs/reference/write_proteomics_releases.html | 2 +- 88 files changed, 198 insertions(+), 105 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2a7ea486..f867b6af 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: MotrpacBicQC Type: Package Title: QC/QA functions for the MoTrPAC community -Version: 0.9.2 -Date: 2024-03-04 +Version: 0.9.3 +Date: 2024-03-25 Author: MoTrPAC Bioinformatics Center Maintainer: David Jimenez-Morales Description: R Package for the analysis of MoTrPAC datasets. diff --git a/NEWS.md b/NEWS.md index 409af1b7..c3f43092 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,15 @@ +# MotrpacBicQC 0.9.3 (2024-03-25) + +* Critical update `validate_refmetname`: ensure checking the refmet standarized name. Update refmet tests +* Update `get_and_validate_mdd()` + + Update REST service url + + Update Documentation + + Remove dependency on data.table +* Enhance: only one `metadata_phase` file allowed +* Enhance `dl_read_gcp`: replace data table by read_delim +* Enhance `open_file`: accept only tab delimited files + + # MotrpacBicQC 0.9.2 (2024-03-04) * Critical Update: Resolved an issue where the validation of refmet names was diff --git a/docs/404.html b/docs/404.html index dfd3d83f..6b3dc7c5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f925ab46..381aa22f 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/articles/index.html b/docs/articles/index.html index f4a6ee48..ca2e4464 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html index a8f94462..64c010b6 100644 --- a/docs/articles/other_functions.html +++ b/docs/articles/other_functions.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Other Functions @@ -123,7 +123,7 @@

MotrpacBicQC: Other Functions

-

2024-03-04

+

2024-03-25

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html index 3c765882..28954ca7 100644 --- a/docs/articles/qc_metabolomics.html +++ b/docs/articles/qc_metabolomics.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Metabolomics QC @@ -126,7 +126,7 @@

MotrpacBicQC: Metabolomics QC

-

2024-03-04

+

2024-03-25

@@ -203,7 +203,11 @@

Usage 
##   + (+) `metabolite_name` OK
##   + (+) `refmet_name` unique values: OK
##   + Validating `refmet_name` (it might take some time)
-
##   + (+) `refmet_name` ids found in refmet: OK
+
##       (-) `refmet_name` [`Leucine/Isoleucine`] must be modified to the RefMet Standarized name: "Leucine" (Error RN2)
+
##       (-) `refmet_name` [`Oxoglutaric acid`] must be modified to the RefMet Standarized name: "2-Oxoglutaric acid" (Error RN2)
+
##       (-) `refmet_name` [`Citric acid/Isocitric acid`] must be modified to the RefMet Standarized name: "Citric acid" (Error RN2)
+
##       (-) Total number of missed ids on MW: 3
+
##    - (-) SUMMARY: 3 `refmet_name` not found in RefMet Metabolomics Data Dictionary: FAIL
##   + (+) {rt} all numeric: OK
##   + (+) {mz} all numeric: OK
##   + (+) {`neutral_mass`} all numeric values OK
diff --git a/docs/articles/qc_olink.html b/docs/articles/qc_olink.html index e4c72e91..a8e3c308 100644 --- a/docs/articles/qc_olink.html +++ b/docs/articles/qc_olink.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: OLINK QC @@ -125,7 +125,7 @@

MotrpacBicQC: OLINK QC

-

2024-03-04

+

2024-03-25

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html index 010e9670..08d5256b 100644 --- a/docs/articles/qc_proteomics.html +++ b/docs/articles/qc_proteomics.html @@ -4,7 +4,7 @@ - + MotrpacBicQC: Proteomics QC @@ -125,7 +125,7 @@

MotrpacBicQC: Proteomics QC

-

2024-03-04

+

2024-03-25

diff --git a/docs/authors.html b/docs/authors.html index f92b7063..09adcbac 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 @@ -82,13 +82,13 @@

Citation

Center MB (2024). MotrpacBicQC: QC/QA functions for the MoTrPAC community. -R package version 0.9.2, https://github.com/MoTrPAC/MotrpacBicQC. +R package version 0.9.3, https://github.com/MoTrPAC/MotrpacBicQC. 

@Manual{,
   title = {MotrpacBicQC: QC/QA functions for the MoTrPAC community},
   author = {MoTrPAC Bioinformatics Center},
   year = {2024},
-  note = {R package version 0.9.2},
+  note = {R package version 0.9.3},
   url = {https://github.com/MoTrPAC/MotrpacBicQC},
 }
diff --git a/docs/index.html b/docs/index.html index 03c479ea..13d08d54 100644 --- a/docs/index.html +++ b/docs/index.html @@ -41,7 +41,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/news/index.html b/docs/news/index.html index dd1cbf52..0c081081 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 @@ -66,6 +66,18 @@

Changelog

Source: NEWS.md +
+

MotrpacBicQC 0.9.3 (2024-03-25)

+
  • Critical update validate_refmetname: ensure checking the refmet standarized name. Update refmet tests
    • +
  • Update get_and_validate_mdd() +
    • Update REST service url
      • +
    • Update Documentation
      • +
    • Remove dependency on data.table
      • +
    • +
  • Enhance: only one metadata_phase file allowed
    • +
  • Enhance dl_read_gcp: replace data table by read_delim
    • +
  • Enhance open_file: accept only tab delimited files
    • +

MotrpacBicQC 0.9.2 (2024-03-04)

  • Critical Update: Resolved an issue where the validation of refmet names was compromised due to updates to the Metabolomics Workbench REST service. This version introduces adjustments to ensure accurate validation of refmet names.
    • diff --git a/docs/notes_developers.html b/docs/notes_developers.html index b710a501..a97b2a12 100644 --- a/docs/notes_developers.html +++ b/docs/notes_developers.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index afc87589..be98a3ac 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: qc_metabolomics: qc_metabolomics.html qc_olink: qc_olink.html qc_proteomics: qc_proteomics.html -last_built: 2024-03-04T17:46Z +last_built: 2024-03-25T18:31Z diff --git a/docs/reference/assay_abbr.html b/docs/reference/assay_abbr.html index 59f4cc26..83238352 100644 --- a/docs/reference/assay_abbr.html +++ b/docs/reference/assay_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html index dc97e62e..c4a57092 100644 --- a/docs/reference/assay_codes.html +++ b/docs/reference/assay_codes.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html index d578f6ae..6dd76b66 100644 --- a/docs/reference/assay_order.html +++ b/docs/reference/assay_order.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html index e238f9b5..109e9bd7 100644 --- a/docs/reference/bic_animal_tissue_code.html +++ b/docs/reference/bic_animal_tissue_code.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_crossfile_olink_validation.html b/docs/reference/check_crossfile_olink_validation.html index 426c5dc5..ce55d9d1 100644 --- a/docs/reference/check_crossfile_olink_validation.html +++ b/docs/reference/check_crossfile_olink_validation.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html index 33e3a12e..618d3b4b 100644 --- a/docs/reference/check_failedsamples.html +++ b/docs/reference/check_failedsamples.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html index 16764508..02aa77e1 100644 --- a/docs/reference/check_manifest_rawdata.html +++ b/docs/reference/check_manifest_rawdata.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html index d3436748..cf6b1b9a 100644 --- a/docs/reference/check_metadata_metabolites.html +++ b/docs/reference/check_metadata_metabolites.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 @@ -114,7 +114,11 @@

Examples

#> + (+) `metabolite_name` OK #> + (+) `refmet_name` unique values: OK #> + Validating `refmet_name` (it might take some time) -#> + (+) `refmet_name` ids found in refmet: OK +#> (-) `refmet_name` [`Leucine/Isoleucine`] must be modified to the RefMet Standarized name: "Leucine" (Error RN2) +#> (-) `refmet_name` [`Oxoglutaric acid`] must be modified to the RefMet Standarized name: "2-Oxoglutaric acid" (Error RN2) +#> (-) `refmet_name` [`Citric acid/Isocitric acid`] must be modified to the RefMet Standarized name: "Citric acid" (Error RN2) +#> (-) Total number of missed ids on MW: 3 +#> - (-) SUMMARY: 3 `refmet_name` not found in RefMet Metabolomics Data Dictionary: FAIL #> + (+) {rt} all numeric: OK #> + (+) {mz} all numeric: OK #> + (+) {`neutral_mass`} all numeric values OK diff --git a/docs/reference/check_metadata_phase_file.html b/docs/reference/check_metadata_phase_file.html index 969fda01..76fbe858 100644 --- a/docs/reference/check_metadata_phase_file.html +++ b/docs/reference/check_metadata_phase_file.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_metadata_proteins.html b/docs/reference/check_metadata_proteins.html index 5dcbdc56..3f5a751a 100644 --- a/docs/reference/check_metadata_proteins.html +++ b/docs/reference/check_metadata_proteins.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html index 55494169..000c1e6c 100644 --- a/docs/reference/check_metadata_samples.html +++ b/docs/reference/check_metadata_samples.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_metadata_samples_olink.html b/docs/reference/check_metadata_samples_olink.html index f9cae71b..109a50b9 100644 --- a/docs/reference/check_metadata_samples_olink.html +++ b/docs/reference/check_metadata_samples_olink.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_missing_values.html b/docs/reference/check_missing_values.html index bd150649..dcaa5e4f 100644 --- a/docs/reference/check_missing_values.html +++ b/docs/reference/check_missing_values.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html index 871fbae5..41e26787 100644 --- a/docs/reference/check_ratio_proteomics.html +++ b/docs/reference/check_ratio_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html index 9caf1853..efa7aa48 100644 --- a/docs/reference/check_results.html +++ b/docs/reference/check_results.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_results_olink.html b/docs/reference/check_results_olink.html index 6070e572..5ca88852 100644 --- a/docs/reference/check_results_olink.html +++ b/docs/reference/check_results_olink.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_rii_proteomics.html b/docs/reference/check_rii_proteomics.html index 6f58ba3a..a4c3971b 100644 --- a/docs/reference/check_rii_proteomics.html +++ b/docs/reference/check_rii_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html index c4be6ef3..017d5dfc 100644 --- a/docs/reference/check_vial_metadata_proteomics.html +++ b/docs/reference/check_vial_metadata_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/check_viallabel_dmaqc.html b/docs/reference/check_viallabel_dmaqc.html index 8cdcc743..68c95b43 100644 --- a/docs/reference/check_viallabel_dmaqc.html +++ b/docs/reference/check_viallabel_dmaqc.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/combine_metabolomics_batch.html b/docs/reference/combine_metabolomics_batch.html index cffe1ffa..ec4bc977 100644 --- a/docs/reference/combine_metabolomics_batch.html +++ b/docs/reference/combine_metabolomics_batch.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/create_folder.html b/docs/reference/create_folder.html index dc2a85e7..e9e2c109 100644 --- a/docs/reference/create_folder.html +++ b/docs/reference/create_folder.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/dl_read_gcp.html b/docs/reference/dl_read_gcp.html index 962c2558..d40d1f14 100644 --- a/docs/reference/dl_read_gcp.html +++ b/docs/reference/dl_read_gcp.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html index 3589f215..8cd517a4 100644 --- a/docs/reference/filter_required_columns.html +++ b/docs/reference/filter_required_columns.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/generate_phase_details.html b/docs/reference/generate_phase_details.html index 53db82a9..d448b019 100644 --- a/docs/reference/generate_phase_details.html +++ b/docs/reference/generate_phase_details.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/get_and_validate_mdd.html b/docs/reference/get_and_validate_mdd.html index 480c437f..4a2cb968 100644 --- a/docs/reference/get_and_validate_mdd.html +++ b/docs/reference/get_and_validate_mdd.html @@ -1,6 +1,6 @@ -Get and validate the entire RefMet database from Metabolomics Workbench — get_and_validate_mdd • MotrpacBicQCGet and Validate the Entire RefMet Database from Metabolomics Workbench — get_and_validate_mdd • MotrpacBicQC @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 @@ -63,33 +63,94 @@
-

Get and validate the entire RefMet database from Metabolomics Workbench

+

Get and Validate the Entire RefMet Database from Metabolomics Workbench

Source: R/metabolomics_data_dictionary.R
-

Get and validate Metabolomics Data Dictionary from -Metabolomics Workbench

+

This function fetches and validates the Metabolomics Data Dictionary +from the Metabolomics Workbench. It provides options to remove duplicates.

- 
get_and_validate_mdd(remove_duplications = FALSE)
+ 
get_and_validate_mdd(remove_duplications = FALSE, verbose = TRUE)

Arguments

remove_duplications
-

(logical) if `TRUE``, removes duplications.

+

Logical; if TRUE, removes duplicate entries based on +the refmet_name column.

+ + +
verbose
+

Logical; if TRUE (default), displays progress messages and warnings +during the function execution.

Value

-

(vector) PHASE code

+

Returns a data frame with the following columns:

refmet_name
+

Character; the name standarized refmet name

+ +
pubchem_cid
+

Character; the PubChem compound ID.

+ +
lm_id
+

Character; the LIPID MAPS ID.

+ +
inchi_key
+

Character; the International Chemical Identifier Key.

+ +
exactmass
+

Numeric; the exact mass of the metabolite.

+ +
formula
+

Character; the chemical formula of the metabolite.

+ +
super_class
+

Character; the superclass category of the metabolite.

+ +
main_class
+

Character; the main class category of the metabolite.

+ +
sub_class
+

Character; the subclass category of the metabolite.

+ +
hmdb_id
+

Character; the Human Metabolome Database ID.

+ +
kegg_id
+

Character; the Kyoto Encyclopedia of Genes and Genomes ID.

+ + +

Each row of the data frame represents a unique metabolite entry from the +Metabolomics Workbench Data Dictionary.

+
+
+

Details

+

This function downloads the entire RefMet database from the Metabolomics +Workbench using their REST API. The data is initially fetched in JSON format and +then converted to a data frame. The function checks for the presence of a 'name' +column in the data frame, renaming it to 'refmet_name' for consistency. It also +provides an option to remove duplicate entries based on the 'refmet_name' column. +If duplicates are found and remove_duplications is FALSE, the function will +list the duplicated IDs but will not remove them. This can be helpful for reviewing +the data quality and consistency.

+
+

Examples

+ 
if (FALSE) {
+  refmet <- get_and_validate_mdd(remove_duplications = TRUE, verbose = TRUE)
+  head(refmet)
+}
+
+
+
diff --git a/docs/reference/group_abbr.html b/docs/reference/group_abbr.html index 222b3c4a..600bf930 100644 --- a/docs/reference/group_abbr.html +++ b/docs/reference/group_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3
diff --git a/docs/reference/group_cols.html b/docs/reference/group_cols.html index 92fe3a77..09a9e145 100644 --- a/docs/reference/group_cols.html +++ b/docs/reference/group_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/index.html b/docs/reference/index.html index c58bd71c..8d7bf39b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 @@ -168,7 +168,7 @@

All functions

get_and_validate_mdd()

-

Get and validate the entire RefMet database from Metabolomics Workbench

+

Get and Validate the Entire RefMet Database from Metabolomics Workbench

get_full_path2batch()

diff --git a/docs/reference/load_metabolomics_batch.html b/docs/reference/load_metabolomics_batch.html index 40c722f2..796f2d11 100644 --- a/docs/reference/load_metabolomics_batch.html +++ b/docs/reference/load_metabolomics_batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/load_olink_batch.html b/docs/reference/load_olink_batch.html index d4cf1b7e..c7f17347 100644 --- a/docs/reference/load_olink_batch.html +++ b/docs/reference/load_olink_batch.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/load_proteomics.html b/docs/reference/load_proteomics.html index 2096e472..4c353fb6 100644 --- a/docs/reference/load_proteomics.html +++ b/docs/reference/load_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/merge_all_metabolomics.html b/docs/reference/merge_all_metabolomics.html index 63dd6c09..a5c52d5f 100644 --- a/docs/reference/merge_all_metabolomics.html +++ b/docs/reference/merge_all_metabolomics.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/merge_metabolomics_metadata.html b/docs/reference/merge_metabolomics_metadata.html index e7ffcd0a..a0bc1ce3 100644 --- a/docs/reference/merge_metabolomics_metadata.html +++ b/docs/reference/merge_metabolomics_metadata.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/merge_phenotype_metabolomics.html b/docs/reference/merge_phenotype_metabolomics.html index 5f375aeb..e3c4275b 100644 --- a/docs/reference/merge_phenotype_metabolomics.html +++ b/docs/reference/merge_phenotype_metabolomics.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/metabolomics_data_dictionary.html b/docs/reference/metabolomics_data_dictionary.html index 2a876bff..994ce929 100644 --- a/docs/reference/metabolomics_data_dictionary.html +++ b/docs/reference/metabolomics_data_dictionary.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/metadata_metabolites_named.html b/docs/reference/metadata_metabolites_named.html index 5364eaa1..abfdbbbe 100644 --- a/docs/reference/metadata_metabolites_named.html +++ b/docs/reference/metadata_metabolites_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/metadata_metabolites_unnamed.html b/docs/reference/metadata_metabolites_unnamed.html index 6185ee22..33f76811 100644 --- a/docs/reference/metadata_metabolites_unnamed.html +++ b/docs/reference/metadata_metabolites_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/metadata_sample_named.html b/docs/reference/metadata_sample_named.html index 00b93bfa..1c8f2554 100644 --- a/docs/reference/metadata_sample_named.html +++ b/docs/reference/metadata_sample_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/metadata_sample_unnamed.html b/docs/reference/metadata_sample_unnamed.html index 80d1a4c3..1624a36c 100644 --- a/docs/reference/metadata_sample_unnamed.html +++ b/docs/reference/metadata_sample_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/open_file.html b/docs/reference/open_file.html index ece8aaf3..2ff1143a 100644 --- a/docs/reference/open_file.html +++ b/docs/reference/open_file.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/phenotypes_pass1a06_short.html b/docs/reference/phenotypes_pass1a06_short.html index 243a0573..f69b70ef 100644 --- a/docs/reference/phenotypes_pass1a06_short.html +++ b/docs/reference/phenotypes_pass1a06_short.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/plot_basic_metabolomics_qc.html b/docs/reference/plot_basic_metabolomics_qc.html index 22eced76..90c07ffe 100644 --- a/docs/reference/plot_basic_metabolomics_qc.html +++ b/docs/reference/plot_basic_metabolomics_qc.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/plot_basic_olink_qc.html b/docs/reference/plot_basic_olink_qc.html index 17117c4a..28db5bda 100644 --- a/docs/reference/plot_basic_olink_qc.html +++ b/docs/reference/plot_basic_olink_qc.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/proteomics_plots_rii.html b/docs/reference/proteomics_plots_rii.html index 07eddbcf..0bdea4db 100644 --- a/docs/reference/proteomics_plots_rii.html +++ b/docs/reference/proteomics_plots_rii.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/remove_empty_columns.html b/docs/reference/remove_empty_columns.html index 6cf666d5..356b5a1a 100644 --- a/docs/reference/remove_empty_columns.html +++ b/docs/reference/remove_empty_columns.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/remove_empty_rows.html b/docs/reference/remove_empty_rows.html index e4f0a7e3..0e5f5dee 100644 --- a/docs/reference/remove_empty_rows.html +++ b/docs/reference/remove_empty_rows.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/results_named.html b/docs/reference/results_named.html index 5bdffcf1..654dc37b 100644 --- a/docs/reference/results_named.html +++ b/docs/reference/results_named.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/results_unnamed.html b/docs/reference/results_unnamed.html index 953f78a4..b9070ba6 100644 --- a/docs/reference/results_unnamed.html +++ b/docs/reference/results_unnamed.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/set_phase.html b/docs/reference/set_phase.html index 2c65b33c..bc691d68 100644 --- a/docs/reference/set_phase.html +++ b/docs/reference/set_phase.html @@ -27,7 +27,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/sex_abbr.html b/docs/reference/sex_abbr.html index c824a9d1..2d70d9dc 100644 --- a/docs/reference/sex_abbr.html +++ b/docs/reference/sex_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/sex_cols.html b/docs/reference/sex_cols.html index db3abbbf..35714094 100644 --- a/docs/reference/sex_cols.html +++ b/docs/reference/sex_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/tissue_abbr.html b/docs/reference/tissue_abbr.html index df52a9cd..bdf28eb5 100644 --- a/docs/reference/tissue_abbr.html +++ b/docs/reference/tissue_abbr.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/tissue_cols.html b/docs/reference/tissue_cols.html index 70205b44..2fa3d40b 100644 --- a/docs/reference/tissue_cols.html +++ b/docs/reference/tissue_cols.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/tissue_order.html b/docs/reference/tissue_order.html index 6dd064c3..dad7f938 100644 --- a/docs/reference/tissue_order.html +++ b/docs/reference/tissue_order.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_assay.html b/docs/reference/validate_assay.html index c847aea2..7b1328af 100644 --- a/docs/reference/validate_assay.html +++ b/docs/reference/validate_assay.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_batch.html b/docs/reference/validate_batch.html index 2a063b11..39c08bb0 100644 --- a/docs/reference/validate_batch.html +++ b/docs/reference/validate_batch.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_cas.html b/docs/reference/validate_cas.html index 9e0454c8..22bc4d10 100644 --- a/docs/reference/validate_cas.html +++ b/docs/reference/validate_cas.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_dates_times.html b/docs/reference/validate_dates_times.html index 947901ba..336cb3ad 100644 --- a/docs/reference/validate_dates_times.html +++ b/docs/reference/validate_dates_times.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_lc_column_id.html b/docs/reference/validate_lc_column_id.html index b216d4d7..131ae37c 100644 --- a/docs/reference/validate_lc_column_id.html +++ b/docs/reference/validate_lc_column_id.html @@ -19,7 +19,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_metabolomics.html b/docs/reference/validate_metabolomics.html index cb7969b5..994e5573 100644 --- a/docs/reference/validate_metabolomics.html +++ b/docs/reference/validate_metabolomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_na_empty.html b/docs/reference/validate_na_empty.html index b2824d5b..7b2349fb 100644 --- a/docs/reference/validate_na_empty.html +++ b/docs/reference/validate_na_empty.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_olink.html b/docs/reference/validate_olink.html index 7b929971..e84740e8 100644 --- a/docs/reference/validate_olink.html +++ b/docs/reference/validate_olink.html @@ -20,7 +20,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_phase.html b/docs/reference/validate_phase.html index db77628d..01dfc452 100644 --- a/docs/reference/validate_phase.html +++ b/docs/reference/validate_phase.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_processFolder.html b/docs/reference/validate_processFolder.html index 7ad21968..982aa9d4 100644 --- a/docs/reference/validate_processFolder.html +++ b/docs/reference/validate_processFolder.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_proteomics.html b/docs/reference/validate_proteomics.html index 18ed0892..55bcefbf 100644 --- a/docs/reference/validate_proteomics.html +++ b/docs/reference/validate_proteomics.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_refmetname.html b/docs/reference/validate_refmetname.html index 10d0b090..0984a983 100644 --- a/docs/reference/validate_refmetname.html +++ b/docs/reference/validate_refmetname.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_tissue.html b/docs/reference/validate_tissue.html index 6f9495a5..60124c2d 100644 --- a/docs/reference/validate_tissue.html +++ b/docs/reference/validate_tissue.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_two_phases.html b/docs/reference/validate_two_phases.html index 9b1eb982..2b29b2b6 100644 --- a/docs/reference/validate_two_phases.html +++ b/docs/reference/validate_two_phases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_uniprot_ids_with_uniprot.html b/docs/reference/validate_uniprot_ids_with_uniprot.html index 75bf97e3..ce0beb58 100644 --- a/docs/reference/validate_uniprot_ids_with_uniprot.html +++ b/docs/reference/validate_uniprot_ids_with_uniprot.html @@ -21,7 +21,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/validate_yyyymmdd_dates.html b/docs/reference/validate_yyyymmdd_dates.html index 4bc05780..5c4d80c8 100644 --- a/docs/reference/validate_yyyymmdd_dates.html +++ b/docs/reference/validate_yyyymmdd_dates.html @@ -17,7 +17,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/write_metabolomics_releases.html b/docs/reference/write_metabolomics_releases.html index cdc8f16c..ad478274 100644 --- a/docs/reference/write_metabolomics_releases.html +++ b/docs/reference/write_metabolomics_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/write_olink_releases.html b/docs/reference/write_olink_releases.html index e254216a..d266496d 100644 --- a/docs/reference/write_olink_releases.html +++ b/docs/reference/write_olink_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3 diff --git a/docs/reference/write_proteomics_releases.html b/docs/reference/write_proteomics_releases.html index a84e16f4..76cd45ea 100644 --- a/docs/reference/write_proteomics_releases.html +++ b/docs/reference/write_proteomics_releases.html @@ -18,7 +18,7 @@ MotrpacBicQC - 0.9.2 + 0.9.3