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Validate the Format and Consistency of a Microbiome Dataset

Source: R/validation_microbiome_dataset.R
check_microbiome_dataset.Rd

This function checks the structure and consistency of various components of a microbiome dataset, including expression data, sample information, variable information, and their respective notes.

Usage

check_microbiome_dataset(
  expression_data,
  sample_info,
  variable_info,
  otu_tree,
  taxa_tree,
  otu_tree_link,
  taxa_tree_link,
  ref_seq,
  sample_info_note,
  variable_info_note
)

Arguments

expression_data

A data frame representing expression data.

sample_info

A data frame containing sample information.

variable_info

A data frame containing variable information.

otu_tree

An optional parameter for OTU tree data.

taxa_tree

An optional parameter for taxa tree data.

An optional explicit mapping between variable_id and otu_tree labels.

An optional explicit mapping between variable_id and taxa_tree labels.

ref_seq

An optional parameter for reference sequence data.

sample_info_note

A data frame containing notes on sample information.

variable_info_note

A data frame containing notes on variable information.

Value

A string "all good." if all checks pass, otherwise returns a descriptive error message indicating the issue found.

Details

The function performs a series of checks to ensure:

  • Required data frames (expression_data, sample_info, variable_info) are provided.

  • All data frames are of the correct class.

  • Key columns exist and there are no duplicated items in critical fields.

  • The dimensions of the data frames are consistent with each other. Errors in these checks will result in descriptive error messages.

Author

Xiaotao Shen xiaotao.shen@outlook.com

Examples

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

check_microbiome_dataset(
  expression_data = global_patterns@expression_data,
  sample_info = global_patterns@sample_info,
  variable_info = global_patterns@variable_info,
  otu_tree = global_patterns@otu_tree,
  taxa_tree = global_patterns@taxa_tree,
  ref_seq = global_patterns@ref_seq,
  sample_info_note = global_patterns@sample_info_note,
  variable_info_note = global_patterns@variable_info_note
)
#> [1] "all good."