spark#

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Last Updated: Mar 11, 2023

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