spark#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_genes.R#L2254

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#

Argument

Description

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)

list()

Additional parameters to the `spark.vc <#spark.vc>`__ function

Details#

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

  • list(“1. CreateSPARKObject?) list(“create a SPARK object from a Giotto object?)

  • list(“2. spark.vc?) list(? Fits the count-based spatial model to estimate the parameters,:raw-latex:n“,? see “, list(list(?spark.vc?)), ? for additional parameters?)

  • list(“3. spark.test?) list(? Testing multiple kernel matrices?)
    Publication: c(“\Sexpr[results=rd]{tools:::Rd_expr_doi(“#1”)}?, “10.1101/810903?) list(“tools:::Rd_expr_doi(“10.1101/810903”)?)

Value#

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