CARD-class: Each CARD object has a number of slots which store...
In YingMa0107/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
CARD-class R Documentation
Each CARD object has a number of slots which store information. Key slots to access
are listed below.
Description
Each CARD object has a number of slots which store information. Key slots to access
are listed below.
Slots
sc_esetThe filtered scRNA-seq data along with meta data stored in the format of SingleCellExperiment.
spatial_countMatThe filtered spatial count data.
spatial_locationThe weights for combining p-values from multiple kernels.
Proportion_CARDThe estimated cell type proportion by CARD with each row is a spatial location and each column is a cell type.
projectThe name of the project, default is deconvolution.
info_parametersThe paramters that are used in model fitting.
algorithm_matrixThe intermediate matrices that are used in the model fitting step.
refined_propThe 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_expressionThe 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.
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| CARD-class | R Documentation |
Each CARD object has a number of slots which store information. Key slots to access are listed below.
Description
Each CARD object has a number of slots which store information. Key slots to access are listed below.
Slots
sc_esetThe filtered scRNA-seq data along with meta data stored in the format of SingleCellExperiment.
spatial_countMatThe filtered spatial count data.
spatial_locationThe weights for combining p-values from multiple kernels.
Proportion_CARDThe estimated cell type proportion by CARD with each row is a spatial location and each column is a cell type.
projectThe name of the project, default is deconvolution.
info_parametersThe paramters that are used in model fitting.
algorithm_matrixThe intermediate matrices that are used in the model fitting step.
refined_propThe 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_expressionThe refined predicted expression matrix (normalized) estimated by CARD for the newly grided spatial locations. The number of initial grids are defined by the user.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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