findMastMarkers_one_vs_all#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/differential_expression.R#L811

Description#

Identify marker feats for all clusters in a one vs all manner based on the MAST package.

Usage#

findMastMarkers_one_vs_all(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  subset_clusters = NULL,
  adjust_columns = NULL,
  pval = 0.001,
  logFC = 1,
  min_feats = 10,
  min_genes = 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

adjust_columns

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

pval

filter on minimal p-value

logFC

filter on logFC

min_feats

minimum feats to keep per cluster, overrides pval and logFC

min_genes

deprecated, use min_feats

verbose

be verbose

...

additional parameters for the zlm function in MAST

Value#

data.table with marker feats

Seealso#

`findMastMarkers <#findmastmarkers>`__