Compute Spatially Variable Genes With SPARK

spark()

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

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

More about SPARK

Details

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

CreateSPARKObject	Creates a SPARK object from a Giotto object
spark.vc	Fits the count-based spatial model to estimate the parameters, see spark.vc for additional parameters
spark.test	Tests multiple kernel matrices

Note

SPARK is a method perceived as an extension of SpatialDE. SPARK models count data directly and employs properly calibrated p-values. Well-calibrated p-values allows this method to find more spatially variable genes at a given FDR cut-off. This is sometimes an improvement over SpatialDE which may produce overly conservative p-values. SPARK models expression levels across spatial locations using generalized linear spatial model (GLSM). It allows modeling the distribution of expression values through an overdispersed Poisson distribution (for count data) or Gaussian distribution (for normalized data). Notably, to make sure that the algorithm can discover various spatial patterns, SPARK employs ten different spatial kernels, including five periodic kernels with different periodicity parameters and five Gaussian kernels with different smoothness parameters.