findMarkers

Source: R/differential_expression.R

Identify marker genes for selected clusters.

findMarkers(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column = NULL,
  method = c("scran", "gini", "mast"),
  subset_clusters = NULL,
  group_1 = NULL,
  group_2 = NULL,
  min_expr_gini_score = 0.5,
  min_det_gini_score = 0.5,
  detection_threshold = 0,
  rank_score = 1,
  min_genes = 4,
  group_1_name = NULL,
  group_2_name = NULL,
  adjust_columns = NULL,
  ...
)

Arguments

gobject

giotto object

expression_values

gene expression values to use

cluster_column

clusters to use

method

method to use to detect differentially expressed genes

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

min_expr_gini_score

gini: filter on minimum gini coefficient for expression

min_det_gini_score

gini: filter minimum gini coefficient for detection

detection_threshold

gini: detection threshold for gene expression

rank_score

gini: rank scores to include

min_genes

minimum number of top genes to return (for gini)

group_1_name

mast: custom name for group_1 clusters

group_2_name

mast: custom name for group_2 clusters

adjust_columns

mast: column in pDataDT to adjust for (e.g. detection rate)

...

additional parameters for the findMarkers function in scran or zlm function in MAST

Value

data.table with marker genes

Details

Wrapper for all individual functions to detect marker genes for clusters.