check_method: Check method input

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

Check method input

Description

Check method input

Usage

check_method(
  method_aggl = NULL,
  method_csr = NULL,
  method_de = NULL,
  method_dist = NULL,
  method_dr = NULL,
  method_gs = NULL,
  method_hclust = NULL,
  method_ovl = NULL,
  method_padj = NULL
)

Arguments

method_aggl	Character value or vector (see details for more). Denotes the agglomerative methods (e.g. 'ward.D') to be used. Run validAgglomerativeMethods() to obtain all valid input options.
method_de	Character value. Denotes the method to according to which the de-analysis is performed. Given to argument test.use of the Seurat::FindAllMarkers()-function. Run SPATA::dea_methods to obtain all valid input options.
method_dist	Character value or vector (see details for more). Denotes the distance methods (e.g. 'euclidean') to be used. Run validDistanceMethods() to obtain all valid input options.
method_dr	Character value. The dimensional reduction method of interest specified as a single character value. (Currently either 'pca', '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_hclust	Character value. Denotes the hierarchical clustering method according to which the clustering is performed. Valid input options are 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' and 'centroid'.
method_ovl	Character value. One of 'classic', 'bayesian'. Decides according to which method the spatial overlap is calculated.
method_padj	Character value. The method according to which the adjusted p-values will be calculated. Given to stats::p.adjust(). Run stats::p.adjust.methods to obtain all valid input options.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.