`spark`¶

spark

Description¶

Compute spatially expressed genes with SPARK method

Usage¶

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

Arguments¶

Argument	Description
`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)
`list()`	Additional parameters to the ``spark.vc` <#spark.vc>`_ function

Details¶

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

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

Value¶

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