Check Integrity and Structure of Microbiome Dataset Object — check_microbiome_dataset

Performs a series of checks on a microbiome dataset object to ensure its integrity and correct structure. This includes verifying the format of various components such as sample_info, variable_info, and expression_data.

Usage

check_microbiome_dataset_class(object)

Arguments

object: A microbiome dataset object to be checked.

Value

TRUE if the dataset passes all checks, otherwise returns a character vector listing the found errors.

Details

The function performs checks to ensure:

variable_info has a variable_id column and no duplicated variable IDs.
sample_info has sample_id and class columns with no duplicated sample IDs.
sample_info_note and variable_info_note have appropriate columns if they exist.
Consistency between the expression_data and the sample_info and variable_info.
Consistency between sample_info, variable_info and their respective notes. Any issues found are returned as character strings in a vector.

Author

Xiaotao Shen xiaotao.shen@outlook.com

Examples

data("global_patterns", package = "microbiomedataset")

check_microbiome_dataset_class(global_patterns)
#> [1] TRUE