findMarkers_one_vs_all#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/differential_expression.R#L1059

Description#

Identify marker feats for all clusters in a one vs all manner.

Usage#

findMarkers_one_vs_all(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  method = c("scran", "gini", "mast"),
  pval = 0.01,
  logFC = 0.5,
  min_feats = 10,
  min_genes = NULL,
  min_expr_gini_score = 0.5,
  min_det_gini_score = 0.5,
  detection_threshold = 0,
  rank_score = 1,
  adjust_columns = NULL,
  verbose = TRUE,
  ...
)

Arguments#

Argument

Description

gobject

giotto object

feat_type

feature type

spat_unit

spatial unit

expression_values

feat expression values to use

cluster_column

clusters to use

subset_clusters

selection of clusters to compare

method

method to use to detect differentially expressed feats

pval

scran & mast: filter on minimal p-value

logFC

scan & mast: filter on logFC

min_feats

minimum feats to keep per cluster, overrides pval and logFC

min_genes

deprecated, use min_feats

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

adjust_columns

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

verbose

be verbose

...

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

Details#

Wrapper for all one vs all functions to detect marker feats for clusters.

Value#

data.table with marker feats

Seealso#

`findScranMarkers_one_vs_all <#findscranmarkersonevsall>`__ , `findGiniMarkers_one_vs_all <#findginimarkersonevsall>`__ and `findMastMarkers_one_vs_all <#findmastmarkersonevsall>`__