generateContingencyTable: Generates a matrix that can directly be used as input for...

In asishallab/GeneFamilies: Analyses different properties of gene families

Generates a matrix that can directly be used as input for hypothesis testing, e.g. with base::fisher.test(...). Validates the resulting table based on the input data. Validation checks whether the intersections of elements having attribute A and B and those having attribute A and NOT B truly form the whole set of all elements with attribute A. The same validation is done for the other rows and columns. Error-Codes are: 1 - row.1 does not fully separate into col.1 and col.2 2 - row.2 does not fully separate into col.1 and col.2 3 - col.1 does not fully separate into row.1 and row.2 4 - col.2 does not fully separate into row.1 and row.2 5 - the sum of all cells sizes in the contingency table is not identical to the size of the mathematical set of all elements contained in both rows and columns (row.1, row.2, col.1, col.2).

Description

Generates a matrix that can directly be used as input for hypothesis testing, e.g. with base::fisher.test(...). Validates the resulting table based on the input data. Validation checks whether the intersections of elements having attribute A and B and those having attribute A and NOT B truly form the whole set of all elements with attribute A. The same validation is done for the other rows and columns. Error-Codes are: 1 - row.1 does not fully separate into col.1 and col.2 2 - row.2 does not fully separate into col.1 and col.2 3 - col.1 does not fully separate into row.1 and row.2 4 - col.2 does not fully separate into row.1 and row.2 5 - the sum of all cells sizes in the contingency table is not identical to the size of the mathematical set of all elements contained in both rows and columns (row.1, row.2, col.1, col.2).

Usage

generateContingencyTable(row.1, row.2, col.1, col.2, row.category,
  col.category, categories = c("T", "F"), validate = TRUE)

Arguments

row.1	a vector of elements that have attribute A
row.2	a vector of elements that do not have attribute A
col.1	a vector of elements that have attribute B
col.2	a vector of elements that do not have attribute B
row.category	the name of attribute A true for elements in row.1 and false for elements in row.2
col.category	the name of attribute B true for elements in col.1 and false for elements in col.2
categories	default is 'T' and 'F' indicating whether row.1 and col.1 indicate elements that have attribute A, and elements in row.2 and col.2 do not have the respective attribute.
validate	set to FALSE, if validation is not wanted. Default is TRUE

Value

A 2 x 2 contingency table.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.