findScranMarkers: findScranMarkers

In drieslab/Giotto_site_suite: 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,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  group_1 = NULL,
  group_1_name = NULL,
  group_2 = NULL,
  group_2_name = NULL,
  verbose = FALSE,
  ...
)

Arguments

gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
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_1_name	custom name for group_1 clusters
group_2	group 2 cluster IDs from cluster_column for pairwise comparison
group_2_name	custom name for group_2 clusters
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 custom selected groups of cells you need to specify the cell_ID column to parameter cluster_column and provide the individual cell IDs to the parameters group_1 and group_2

By default group names will be created by pasting the different id names within each selected group. When you have many different ids in a single group it is recommend to provide names for both groups to group_1_name and group_2_name

Value

data.table with marker genes

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.