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