check_method: Check method input

In kueckelj/SPATA: A Toolbox for Spatial Gene Expression Analysis

Check method input

Description

A member of the lazy-check_*()-family.

Usage

check_method(
  method_dr = NULL,
  method_gs = NULL,
  method_de = NULL,
  method_padj = NULL,
  method_ovl = NULL
)

Arguments

method_dr	Character value. The dimensional reduction method of interest specified as a single character value. (Currently either 'UMAP' or 'TSNE').
method_gs	Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean' or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA().
method_de	Character value. Given to argument test.use of Seurat::FindAllMarkers().
method_padj	Character value. The method according to which the adjusted p-values will be calculated. Given to stats::p.adjust().
method_ovl	Character value. One of 'classic', 'bayesian'. Decides according to which method the spatial overlap is calculated.

Details

Members of the lazy-check_*()-family take the arguments of their kind - that are used in the function they are called in - and checks whether these arguments input fit the requirements. They stop and return an error immediately once they stumble upon something invalid. They do not alter or adjust input and return TRUE if the whole function has been executed without anything invalid being found.

Value

A logical value TRUE if nothing invalid has been detected or an informative error message.

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.