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

In YingMa0107/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

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

Description

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

Slots

spatial_countMat

The filtered spatial count data.

spatial_location

The weights for combining p-values from multiple kernels.

Proportion_CARD

The estimated cell type proportion by CARD with each row is a spatial location and each column is a cell type.

estimated_refMatrix

The estimated reference matrix by CARDfree with each row represents a gene and each column represents a cell type cluster.

project

The name of the project, default is deconvolution.

markerList

The nlist of cell type specific markers, with each element represents the vector of cell type specific markers

info_parameters

The paramters that are used in model fitting.

algorithm_matrix

The intermediate matrices that are used in the model fitting step.

refined_prop

The refined cell type proportion matrix estimated by CARD for the newly grided spatial locations. The number of initial grids are defined by the user.

refined_expression

The refined predicted expression matrix (normalized) estimated by CARD for the newly grided spatial locations. The number of initial grids are defined by the user.

YingMa0107/CARD documentation built on Feb. 14, 2024, 12:23 p.m.