findScranMarkers

Identify marker genes for all or selected clusters based on scran's implementation of findMarkers.

findScranMarkers(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  group_1 = NULL,
  group_2 = NULL,
  verbose = FALSE,
  ...
)

Arguments

gobject

giotto object

expression_values

gene expression values to use

cluster_column

clusters to use

subset_clusters

selection of clusters to compare

group_1

group 1 cluster IDs from cluster_column for pairwise comparison

group_2

group 2 cluster IDs from cluster_column for pairwise comparison

verbose

be verbose (default = FALSE)

...

additional parameters for the findMarkers function in scran

Value

data.table with marker genes

Details

This is a minimal convenience wrapper around the findMarkers function from the scran package.

To perform differential expression between cluster groups you need to specificy cluster IDs to the parameters group_1 and group_2.

Examples

data(mini_giotto_single_cell)

scran_markers = findScranMarkers(gobject = mini_giotto_single_cell,
                                 cluster_column = 'leiden_clus',
                                 group_1 = 1,
                                 group_2 = 2)