Package index • MotrpacBicQC

All functions

assay_abbr: assay abbreviations

assay_codes: Motrpac assay codes

assay_order: assay order

bic_animal_tissue_code: BIC Tissue Code and Name

check_crossfile_validation(): Cross-validate assay files (Olink and LAB)

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_analyte(): Check analyte metadata file

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_lab(): Check LAB metadata samples file

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_assays(): Check results file for assays

check_rii_proteomics(): check proteomics reported ion intensity file

check_vial_metadata_proteomics(): check proteomics vial metadata file

check_viallabel_dmaqc(): Validate vial labels from DMAQC

clean_character_columns(): Clean character columns

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 Workbench

get_full_path2batch(): Get full path to the batch folder

group_abbr: group abbreviations

group_cols: group colors

load_lab_batch(): Load and Process LAB Batch Data

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_lab_qc(): Generate Basic LAB QC Plots

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_lab(): Validate LAB Assay Data

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_lab_releases(): Write LAB Data Release

write_metabolomics_releases(): Write metabolomics data release

write_olink_releases(): Write olink data release

write_proteomics_releases(): Write proteomics data release