QA functions for the MoTrPAC community

assay_abbr	assay abbreviations
assay_codes	Motrpac assay codes
assay_order	assay order
bic_animal_tissue_code	BIC Tissue Code and Name
check_crossfile_olink_validation	Cross-validate OLINK files
check_failedsamples	check failed samples file for reported missing vial label ids
check_manifest_rawdata	check rawfiles between manifest and metabolite_sample matches
check_metadata_metabolites	check metadata metabolites
check_metadata_phase_file	check metadata phase file
check_metadata_proteins	Check olink metadata proteins file
check_metadata_samples	check metadata samples
check_metadata_samples_olink	check olink metadata samples file
check_missing_values	Check for Missing Values in a Data Frame Column
check_ratio_proteomics	check proteomics ratio file
check_results	check results
check_results_olink	Check olink results
check_rii_proteomics	check proteomics reported ion intensity file
check_viallabel_dmaqc	Validate vial labels from DMAQC
check_vial_metadata_proteomics	check proteomics vial metadata file
combine_metabolomics_batch	Combines all files from a Metabolomics batch
create_folder	Create folder
dl_read_gcp	Download and Read File from Google Cloud Storage
filter_required_columns	filter required columns only
generate_phase_details	Generate the phase detail for submissions
get_and_validate_mdd	Get and Validate the Entire RefMet Database from Metabolomics...
get_full_path2batch	Get full path to the batch folder
group_abbr	group abbreviations
group_cols	group colors
load_metabolomics_batch	Load metabolomics batch
load_olink_batch	Load and Process Olink Batch Data
load_proteomics	Load Proteomics batch
merge_all_metabolomics	Merge all metabolomics files
merge_metabolomics_metadata	Merge metabolomics metadata named and unnamed
merge_phenotype_metabolomics	Merge phenotypic and metabolics results
metabolomics_data_dictionary	Metabolomics data dictionary
metadata_metabolites_named	Metadata Metabolites test dataset for NAMED metabolites
metadata_metabolites_unnamed	Metadata Metabolites test dataset for UNNAMED metabolites
metadata_sample_named	Metadata Sample test dataset for NAMED metabolites
metadata_sample_unnamed	Metadata Sample test dataset for UNNAMED metabolites
open_file	open files
phenotypes_pass1a06_short	Motrpac Phenotypes PASS1A 6 Months
plot_basic_metabolomics_qc	Plot Basic Metabolomics QC charts
plot_basic_olink_qc	Plot Basic OLINK QC charts
proteomics_plots_rii	QC Plot of proteomics reporter ion intensity data
remove_empty_columns	remove empty columns
remove_empty_rows	remove empty rows in data frame
results_named	Results test dataset for NAMED metabolites
results_unnamed	Results test dataset for UNNAMED metabolites
set_phase	Set the phase to be validated.
sex_abbr	sex abbreviations
sex_cols	sex colors
tissue_abbr	tissue abbreviations
tissue_cols	tissue colors
tissue_order	tissue order
validate_assay	extract ASSAY from input folder path
validate_batch	extract BATCH_YYYYMMDD folder
validate_cas	validate cas code
validate_dates_times	Validate date-time format in a data frame column
validate_lc_column_id	Validate 'lc_column_id' column
validate_metabolomics	Validate a Metabolomics submission
validate_na_empty	Validate Column for NA and Empty Values
validate_olink	Validate Olink Data
validate_phase	Extract PHASE from input folder path
validate_processFolder	extract PROCESSED_YYYYMMDD folder from input folder path
validate_proteomics	Validate a Proteomics submissions
validate_refmetname	Validate refmet_name
validate_tissue	extract and validate TISSUE CODE from input folder path
validate_two_phases	validate a phase with two phases (pass1a and 1c)
validate_uniprot_ids_with_uniprot	Validate UniProt IDs
validate_yyyymmdd_dates	Validate YYYY-MM-DD Dates in a Data Frame
write_metabolomics_releases	Write metabolomics data release
write_olink_releases	Write olink data release
write_proteomics_releases	Write proteomics data release