findMastMarkers: findMastMarkers

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Identify marker genes for selected clusters based on the MAST package.

Usage

findMastMarkers(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  group_1 = NULL,
  group_1_name = NULL,
  group_2 = NULL,
  group_2_name = NULL,
  adjust_columns = NULL,
  verbose = FALSE,
  ...
)

Arguments

gobject	giotto object
expression_values	gene expression values to use
cluster_column	clusters to use
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
adjust_columns	column in pDataDT to adjust for (e.g. detection rate)
verbose	be verbose
...	additional parameters for the zlm function in MAST

Details

This is a minimal convenience wrapper around the zlm from the MAST package to detect differentially expressed genes.

Value

data.table with marker genes

Examples

    findMastMarkers(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.