findScranMarkers: findScranMarkers

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

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

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 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)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.