Identify Marker Genes Based on Scran

findScranMarkers()

Identify marker genes for all or selected clusters based on scran’s implementation of `findMarkers <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

A 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 specify 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)