findDE.Rd
Finds the differentially expressed genes across a set of subgroups.
findDE( object, of_sample = "", across, across_subset = NULL, method_de = "wilcox", p_val_adj = 0.05 )
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 |
across_subset | Character vector or NULL. Specify the particular groups or clusters of interest the feature-variable
specified in argument Hint: Use |
method_de | Character value. Given to argument |
p_val_adj | The maximum adjusted p-value allowed in the output. |
A data.frame containing the variables 'p_val', 'avg_logFC', 'pct.1', 'pct.2', 'p_val_adj', 'cluster', 'gene'.