findMastMarkers_one_vs_all

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

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

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

See also

findMastMarkers

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

findMastMarkers_one_vs_all(gobject = g, cluster_column = "leiden_clus")
#> Error: package 'MAST' is not yet installed
#> 
#>  To install:
#> if(!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager');
#> BiocManager::install(c("MAST"))