findScranMarkers#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/differential_expression.R#L31

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#

Argument

Description

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 <#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