spark — spark • Giotto

Compute spatially expressed genes with SPARK method

spark(
  gobject,
  percentage = 0.1,
  min_count = 10,
  expression_values = "raw",
  num_core = 5,
  covariates = NULL,
  return_object = c("data.table", "spark"),
  ...
)

Arguments

gobject: giotto object
percentage: The percentage of cells that are expressed for analysis
min_count: minimum number of counts for a gene to be included
expression_values: type of values to use (raw by default)
num_core: number of cores to use
covariates: The covariates in experiments, i.e. confounding factors/batch effect. Column name of giotto cell metadata.
return_object: type of result to return (data.table or spark object)
...: Additional parameters to the spark.vc function

Value

data.table with SPARK spatial genes results or the SPARK object

Details

This function is a wrapper for the method implemented in the SPARK package:

1. CreateSPARKObject create a SPARK object from a Giotto object
2. spark.vc Fits the count-based spatial model to estimate the parameters, see spark.vc for additional parameters
3. spark.test Testing multiple kernel matrices