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