findDE: Find marker genes

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

Find marker genes

Description

Finds the differentially expressed genes across a set of subgroups.

Usage

findDE(
  object,
  of_sample = "",
  across,
  across_subset = NULL,
  method_de = "wilcox",
  p_val_adj = 0.05
)

Arguments

object	A valid spata-object.
of_sample	The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
across	Character value. The name of the discrete feature-variable of interest. Hint: Character- or factor- variables are discrete variables. These functionally assign the barcode spots to distinct groups or clusters (e.g. segment or seurat_clusters) whoose properties you might want to compare against each other. Use getFeatureNames() to get an overview of the features variables your spata-object contains.
across_subset	Character vector or NULL. Specify the particular groups or clusters of interest the feature-variable specified in argument across contains. If set to NULL all of them are chosen. Hint: Use getFeatureValues() to obtain all available groups of a certain feature-variable.
method_de	Character value. Given to argument test.use of Seurat::FindAllMarkers().
p_val_adj	The maximum adjusted p-value allowed in the output.

Value

A data.frame containing the variables 'p_val', 'avg_logFC', 'pct.1', 'pct.2', 'p_val_adj', 'cluster', 'gene'.

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