`findScranMarkers`¶

findScranMarkers

Description¶

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

Usage¶

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

Arguments¶

Argument	Description
`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

Details¶

This is a minimal convenience wrapper around

the ``findMarkers` <#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 .

Value¶

data.table with marker genes

Examples¶

data(mini_giotto_single_cell)

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

findScranMarkers¶