spark#

Last Updated: Jan 29, 2024

Description#

Compute spatially expressed genes with SPARK method

Usage#

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

Arguments#

`gobject`	giotto object
`spat_loc_name`	name for spatial locations
`feat_type`	feature type
`spat_unit`	spatial unit
`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

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
1. spark.test Testing multiple kernel matrices

Publication: doi:10.1101/810903

Value#

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