spark.vc: Fitting the count-based spatial model to estimate the...
In xzhoulab/SPARK: Spatial Pattern Recognition via Kernels

spark.vc

R Documentation

Fitting the count-based spatial model to estimate the parameters

Description

Fitting the count-based spatial model to estimate the parameters

Usage

spark.vc(
  object,
  covariates = NULL,
  lib_size = NULL,
  fit.maxiter = 500,
  fit.tol = 1e-05,
  fit.model = "poisson",
  num_core = 1,
  verbose = FALSE
)

Arguments

`object`	SPARK object
`covariates`	The covariates in experiments, i.e. confounding factors/batch effect
`lib_size`	The read depth for each cell
`fit.maxiter`	Iteration
`fit.tol`	Tolerance
`fit.model`	The model to be either "poisson" or "gaussian"
`num_core`	The number of core used when fitting the model
`verbose`	Output fitting information