findMarkers_one_vs_all

Source: R/differential_expression.R

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

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

Arguments

gobject

giotto object

expression_values

gene expression values to use

cluster_column

clusters to use

subset_clusters

selection of clusters to compare

method

method to use to detect differentially expressed genes

pval

scran & mast: filter on minimal p-value

logFC

scan & mast: filter on logFC

min_genes

minimum genes to keep per cluster, overrides pval and logFC

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

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

Value

data.table with marker genes

Details

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