findMarkers#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/differential_expression.R#L947

Description#

Identify marker feats for selected clusters.

Usage#

findMarkers(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  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_feats = 4,
  min_genes = NULL,
  group_1_name = NULL,
  group_2_name = NULL,
  adjust_columns = NULL,
  ...
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

expression_values

feat expression values to use

cluster_column

clusters to use

method

method to use to detect differentially expressed feats

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 feat expression

rank_score

gini: rank scores to include

min_feats

minimum number of top feats to return (for gini)

min_genes

deprecated, use min_feats

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

Details#

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

Value#

data.table with marker feats

Seealso#

`findScranMarkers <#findscranmarkers>`__ , `findGiniMarkers <#findginimarkers>`__ and `findMastMarkers <#findmastmarkers>`__