spark | R Documentation |
Compute spatially expressed genes with SPARK method
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"),
...
)
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 |
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
Publication: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/810903")}
data.table with SPARK spatial genes results or the SPARK object
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