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Distribution of the Data Set Shown by Skewness and Kurtosis.

Source: R/cyt_skku.R
cyt_skku.Rd

This function computes summary statistics — including sample size, mean, standard error, skewness, and kurtosis — for each numeric measurement column in a data set. If grouping columns are provided via group_cols, the function computes the metrics separately for each group defined by the combination of these columns (using the first element as the treatment variable and the second as the grouping variable, or the same column for both if only one is given). When no grouping columns are provided, the entire data set is treated as a single group ("Overall"). A log2 transformation (using a cutoff equal to one-tenth of the smallest positive value in the data) is applied to generate alternative metrics. Histograms showing the distribution of skewness and kurtosis for both raw and log2-transformed data are then generated and saved to a PDF if a file name is provided.

Usage

cyt_skku(
  data,
  group_cols = NULL,
  pdf_title = NULL,
  print_res_raw = FALSE,
  print_res_log = FALSE
)

Arguments

data

A matrix or data frame containing the raw data. If group_cols is specified, the columns with names in group_cols are treated as grouping variables and all other columns are assumed to be numeric measurement variables.

group_cols

A character vector specifying the names of the grouping columns. When provided, the first element is treated as the treatment variable and the second as the group variable. If not provided, the entire data set is treated as one group.

pdf_title

A character string specifying the file name for the PDF file in which the histograms will be saved. If NULL, the histograms are displayed on the current graphics device. Default is NULL.

print_res_raw

Logical. If TRUE, the function returns and prints the computed summary statistics for the raw data. Default is FALSE.

print_res_log

Logical. If TRUE, the function returns and prints the computed summary statistics for the log2-transformed data. Default is FALSE.

Value

The function generates histograms of skewness and kurtosis for both raw and log2-transformed data. Additionally, if either printResRaw and/or printResLog is TRUE, the function returns the corresponding summary statistics as a data frame or a list of data frames.

Details

A cutoff is computed as one-tenth of the minimum positive value among all numeric measurement columns to avoid taking logarithms of zero. When grouping columns are provided, the function loops over unique grouping columns and computes the metrics for each measurement column within each subgroup. Without grouping columns, the entire data set is analyzed as one overall group.

Examples

# Example with grouping columns (e.g., "Group" and "Treatment")
data(ExampleData1)
cyt_skku(ExampleData1[, -c(2:3)], pdf_title = NULL,
  group_cols = c("Group")
)
#> Warning: Removed 2 rows containing non-finite outside the scale range (`stat_bin()`).
#> Warning: Removed 2 rows containing non-finite outside the scale range (`stat_bin()`).


# Example without grouping columns (analyzes the entire data set)
cyt_skku(ExampleData1[, -c(1:3)], pdf_title = NULL)