mcmcChain: Read MCMC chain associated with a BayesSpace clustering or...
In BayesSpace: Clustering and Resolution Enhancement of Spatial Transcriptomes
Description
Usage
Arguments
Details
Value
Examples
Description
BayesSpace stores the MCMC chain associated with a clustering or enhancement
on disk in an HDF5 file. The mcmcChain() function reads any parameters
specified by the user into a coda::mcmc object compatible with
TidyBayes.
Usage
1
2
3
mcmcChain(sce, params = NULL)
removeChain(sce)
Arguments
sce
SingleCellExperiment with a file path stored in its metadata.
params
List of model parameters to read
Details
To interact with the HDF5 file directly, obtain the filename from the
SingleCellExperiment's metadata: metadata(sce)$chain.h5. Each
parameter is stored as a separate dataset in the file, and is represented as
a matrix of size (n_iterations x n_parameter_indices).
Value
Returns an mcmc object containing the values of the requested
parameters over the constructed chain.
Examples
1
2
3
4
5
set.seed(149)
sce <- exampleSCE()
sce <- spatialCluster(sce, 7, nrep=100, burn.in=10, save.chain=TRUE)
chain <- mcmcChain(sce)
removeChain(sce)
BayesSpace documentation built on Nov. 8, 2020, 8:03 p.m.
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Description Usage Arguments Details Value Examples
Description
BayesSpace stores the MCMC chain associated with a clustering or enhancement
on disk in an HDF5 file. The mcmcChain() function reads any parameters
specified by the user into a coda::mcmc object compatible with
TidyBayes.
Usage
1 2 3 | mcmcChain(sce, params = NULL)
removeChain(sce)
|
Arguments
sce |
SingleCellExperiment with a file path stored in its metadata. |
params |
List of model parameters to read |
Details
To interact with the HDF5 file directly, obtain the filename from the
SingleCellExperiment's metadata: metadata(sce)$chain.h5. Each
parameter is stored as a separate dataset in the file, and is represented as
a matrix of size (n_iterations x n_parameter_indices).
Value
Returns an mcmc object containing the values of the requested
parameters over the constructed chain.
Examples
1 2 3 4 5 | set.seed(149)
sce <- exampleSCE()
sce <- spatialCluster(sce, 7, nrep=100, burn.in=10, save.chain=TRUE)
chain <- mcmcChain(sce)
removeChain(sce)
|
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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