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"), ... )
| 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 |
data.table with SPARK spatial genes results or the SPARK object
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
3. spark.test Testing multiple kernel matrices