`findScranMarkers`¶

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¶

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

findScranMarkers¶