spark#
Last Updated: Oct 02, 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#
|
giotto object |
|
name for spatial locations |
|
feature type |
|
spatial unit |
|
The percentage of cells that are expressed for analysis |
|
minimum number of counts for a gene to be included |
|
type of values to use (raw by default) |
|
number of cores to use |
|
The covariates in experiments, i.e. confounding factors/batch effect. Column name of giotto cell metadata. |
|
type of result to return (data.table or spark object) |
|
Additional parameters to the
|
Details#
This function is a wrapper for the method implemented in the SPARK package:
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 parametersspark.test Testing multiple kernel matrices
Publication: doi:10.1101/810903
Value#
data.table with SPARK spatial genes results or the SPARK object