calculate_cv {MetAlyzer}

Add mean, SD and CV

Description

This function calculates the mean, standard deviation (SD) and the coefficient of variation (CV) for each group and adds them to aggregated_data.

Usage

calculate_cv(
  metalyzer_se,
  groups = NULL,
  cv_thresholds = c(0.1, 0.2, 0.3),
  na.rm = TRUE
)

Arguments

metalyzer_se

A Metalyzer object

groups

A vector of column names of aggregated_data to calculate mean, SD and CV group wise. If the column does not exists in aggregated_data it is automatically added from meta data. The default value is set to NULL, which uses the existing grouping of aggregated_data.

cv_thresholds

A numeric vector of upper thresholds (CV <= t) between 0 and 1 for CV categorization.

na.rm

a logical evaluating to TRUE or FALSE indicating whether NA values should be stripped before the computation proceeds.

Value

An updated aggregated_data tibble data frame

Examples

metalyzer_se <- MetAlyzer_dataset(file_path = example_extraction_data())
metalyzer_se <- renameMetaData(
  metalyzer_se,
  Extraction_Method = "Sample Description"
)
metalyzer_se <- filterMetaData(
  metalyzer_se,
  Tissue == "Drosophila"
)
metalyzer_se <- calculate_cv(
  metalyzer_se,
  groups = c("Tissue", "Extraction_Method", "Metabolite"),
  cv_thresholds = c(0.1, 0.2, 0.3),
  na.rm = TRUE
)