find_dge_variables: Find genes that meet selected differential expression...

In drewvoigt10/cellcuratoR: Shares Interactive Single-Cell Visualizations from Seurat

Find genes that meet selected differential expression thresholds

Description

find_dge_variables returns a vector of genes that satisfy differential expression threshold criteria (log fold-change and min.pct thresholds). This allows for differential expression to be conducted in a loop and a progress bar to display within the shiny app indiciating the progress of the (sometimes lengthy) differential expression. It is modified from the Seurat FindMarkers() function.

Usage

find_dge_variables(object, ident.1, ident.2, my_logfc_threshold,
  my_minpct_threshold)

Arguments

object	Seurat S4 object. The active identity of the object should match the ident.1 and ident.2 parameters. You can switch the identity of your Seurat object with Idents(object) <- my_ident.
ident.1	Identity class for group-1 for differential expression.
ident.2	Optional identity class for group-2 for differential expression.If differential expression should be compared to all other cells, leave ident.2 empty.
my_logfc_threshold	The log fold-change threshold that will limit differential expression testing to genes with expression differences greater than the specified log fold-change threshold. Only genes with a log fold-change threshold of greater than my_logfc_threshold will be returned.
my_minpct_threshold	The cutoff for the proportion of cells that express the gene of interest. Only genes that are expressed in a greater proportion of cells than the my_minpct_threshold will be returned.

Examples

## Not run: 
find_dge_variables(seurat_obj, ident.1 = 2, ident.2 = c(3,4),
my_logfc_threshold = 0.25, my_minpct_threshold = 0.5)
find_dge_variables(seurat_obj, ident.1 = 3, my_logfc_threshold = 0.5,
my_minpct_threshold = 0.1)

## End(Not run)

drewvoigt10/cellcuratoR documentation built on May 22, 2023, 4:38 p.m.