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Unify and Format Metadata

Source: R/unify_metadata.R
unify_metadata.Rd

This function merges and formats metadata from various sources, including QIIME metadata, experimental sample metadata, and qPCR or FCM data, to create a unified metadata file for downstream analyses.

Usage

unify_metadata(projects)

Arguments

projects

A character vector containing the names of the project (folders).

Value

A data frame containing the unified metadata. The data frame is also saved as a file in the project's input_data folder.

Details

The function ensures that the metadata is unified and correctly formatted for further analysis by:

  • Reading and processing the metadata_extra.tsv file, which must contain at least:

    • SampleID: A unique identifier for each sample.

    • sample_type: Indicates whether the sample is a sample, mock, or blank.

    • DNA_Concentration: The DNA concentration (in ng/µl).

  • Optionally processing and integrating qPCR or FCM data:

    • If qPCR data is available, calculating the mean for duplicates and merging it with metadata_extra.

    • If FCM data is available, calculating the mean for duplicates and merging it with metadata_extra.

  • Reading the metadata.tsv file (QIIME metadata), ensuring it contains the SampleID column, and combining it with the processed metadata_extra.

  • Writing the final combined metadata to a file. Note that the output file is named by concatenating the project name with _metadata_formatted.tsv and is saved in the project's input_data folder.

All metadata files (QIIME metadata, experimental sample metadata, and qPCR/FCM data) must include the SampleID column for proper merging. This column serves as the key to align data from multiple sources.

Note

This function requires that the folder structure has been set up (using the create_folders function) before running.

Examples

if (FALSE) { # \dontrun{
# Process and unify metadata for a project
unified_metadata <- unify_metadata(projects)
} # }