sparkx: The main function that testing multiple kernels with...
In xzhoulab/SPARK: Spatial Pattern Recognition via Kernels

sparkx

R Documentation

The main function that testing multiple kernels with non-parametric framework

Description

SPARK-X builds on the covariance kernel test framework, identifying genes with spatial expression pattern in large scale patial transcriptomic studies

Usage

sparkx(
  count_in,
  locus_in,
  X_in = NULL,
  numCores = 1,
  option = "mixture",
  verbose = TRUE
)

Arguments

`count_in:`	A n x p gene expression matrix (sparseMatrix)
`locus_in:`	A n x d location matrix
`X_in:`	A n x c covariate matrix
`numCores:`	A integer specifying multiple threads
`option:`	A description of kernels to be tested, "single", only tests for projection kernels; "mixture", tests for additional ten kernels.
`verbose:`	A boolean value whether to print details, for debug purpose

Value

A list of estimated parameters

`stats`	A n x k matrix of test statistics for all kernels
`res_stest`	A n x k matrix of P values for all kernels
`res_mtest`	A n x 2 matrix of combined P values and BY-adjusted P values