Summarize Samples in a Microbiome Dataset

This generic function summarizes the expression data in a microbiome dataset object based on specified criteria like mean, median, or sum of intensities, grouped by a specified factor.

Specific implementation of summarise_samples for objects of class microbiome_dataset. It performs the summarization of expression data based on the specified criteria and grouping.

Usage

summarise_samples(
  object,
  what = c("mean_intensity", "median_intensity", "sum_intensity"),
  group_by,
  ...
)

summarize_samples(
  object,
  what = c("mean_intensity", "median_intensity", "sum_intensity"),
  group_by,
  ...
)

# S3 method for class 'microbiome_dataset'
summarise_samples(
  object,
  what = c("sum_intensity", "mean_intensity", "median_intensity"),
  group_by,
  ...
)

Arguments

object

A microbiome dataset object of class microbiome_dataset.

what

A character string specifying the type of summary required. Options are "mean_intensity", "median_intensity", or "sum_intensity". Default is "mean_intensity".

group_by

A character string specifying the grouping variable.

...

Additional arguments.

Value

A modified microbiome dataset object with summarized expression data.

A microbiome dataset object with updated sample_info and expression_data reflecting the summarization.

Details

The summarise_samples function is a generic method, which calls the appropriate method (e.g., summarise_samples.microbiome_dataset) based on the class of the object. It summarizes the expression data based on the given what parameter and groups by group_by.

This method specifically handles objects of the microbiome_dataset class. It applies the summarization as specified by the what and group_by parameters and updates the object accordingly.

Examples

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

x <- summarise_samples(
  object = global_patterns,
  what = "sum_intensity",
  group_by = "SampleType"
)
dim(x@expression_data)
#> [1] 19216     9