SPARK-class: Each SPARK object has a number of slots which store...

In xzhoulab/SPARK: Spatial Pattern Recognition via Kernels

Each SPARK object has a number of slots which store information. Key slots to access are listed below.

Description

Each SPARK object has a number of slots which store information. Key slots to access are listed below.

Slots

counts

The raw expression count matrix

scaled_counts

Scaled (default is variance stabilizing transformation for each gene) expression matrix; used for visualization

weights

The weights for combining p-values from multiple kernels

kernelmat

The kernel matrix for spatial gene recognization, a list

lib_size

The total read depth for each cell

fit_model

The model to be fitted, either "poisson" or "gaussian"

num_core

The number of core used in the package

location

Cell corrdinates to compute the kernel matrix

project

Name of the project (for record keeping)

res_vc

The results for variance component estimation step

res_stest

The results for variance component testing step for each kernel

res_mtest

The results for variance component testing step for combined multiple kernels

xzhoulab/SPARK documentation built on Nov. 20, 2022, 2:54 p.m.