Package index • parkinsonsMetagenomicData

All functions

accessParquetData(): Set up DuckDB connection with views for available data types

add_metadata(): Add sample metadata to TreeSummarizedExperiment object as colData

biobakery_files(): Read in extdata/biobakery_file_definitions.csv

cacheMetagenomicData(): Retrieve and cache output files

cache_gcb(): Cache Google Bucket object

confirm_data_type(): Validate 'data_type' argument

confirm_duckdb_con(): Validate DuckDB connection argument

confirm_duckdb_view(): Validate DuckDB view/table argument

confirm_filter_values(): Validate 'filter_values' argument

confirm_repo() confirm_ref(): Validate 'repo' argument

confirm_uuids(): Validate UUIDs

db_connect(): Connect to DuckDB database instance

detect_data_type(): Detect which accepted data type a string is referring to

file_to_hf(): Convert standard https:// URLs to httpfs-compatible hf:// URLs

filter_parquet_view(): Filter a database view by any number of column:value argument pairs

get_bucket_locators(): Retrieve Google Bucket locators for output

get_cdata_only(): Return unique colData columns for a data type

get_exts(): Return all "extensions" from a file path

get_hf_parquet_urls(): Get Parquet File URLs and Metadata from a Hugging Face Repository

get_ref_info(): Return a table with information about available parquet reference files.

get_repo_info(): Return a table with information about available Hugging Face repos.

interpret_and_filter(): Select the view with the most appropriate sorting schema and filter

listMetagenomicData(): List metagenomic data available for download

loadMetagenomicData(): Load cached files into R as a merged TreeSummarizedExperiment object

loadParquetData(): Retrieve data from a DuckDB view and convert to Summarized Experiment

load_ref(): Load a single parquet reference file

mergeExperiments(): Merge TreeSummarizedExperiment objects with the same assay types together

output_file_types(): Read in extdata/output_files.csv

pMD_get_cache(): Get location of dedicated file cache

parquet_colinfo(): Retrieve column info for parquet files based on original file type

parquet_to_tse(): Convert tabulated parquet file data to a Summarized Experiment

parse_fastqc_stats(): Parse FastQC data file for a single sample as a named vector

parse_humann(): Parse HUMAnN output for a single sample as a TreeSummarizedExperiment object

parse_kneaddata_stats(): Parse KneadData log file for a single sample as a named vector

parse_metaphlan_list(): Parse basic MetaPhlAn output for a single sample as a TreeSummarizedExperiment object

pick_projection(): Choose the most appropriate DuckDB view/table for filtering

retrieve_local_views(): Create database views from local parquet files

retrieve_views(): Create database views for all available or requested data types

returnSamples(): Return a TreeSummarizedExperiment with data based on sample data and feature data tables

sampleMetadata: Manually Curated Sample Metadata

standardize_ordering(): Standardize the order of a vector of delimited strings

view_parquet(): Create a database view of a specific parquet file