scmet_to_sce: Convert from scmet to SingleCellExperiment object.
In andreaskapou/scMET: Bayesian modelling of cell-to-cell DNA methylation heterogeneity
scmet_to_sce R Documentation
Convert from scmet to SingleCellExperiment object.
Description
Helper function that converts an scmet to SCE object. The
structure of the SCE object to store single cell methylation data is the
following. We create two assays, met storing methylated CpGs and total
storing total number of CpGs. Rows correspond to features and columns to
cells, similar to scRNA-seq convention. The rownames and colnames slots
should store the feature and cell names, respectively. Covariates X
that might explain variability in mean (methylation) should be stored
in metadata(rowData(sce)$X.
Usage
scmet_to_sce(Y, X = NULL)
Arguments
Y
Methylation data in data.table format.
X
(Optional) Matrix of covariates.
Value
An SCE object with the structure described above.
Author(s)
C.A.Kapourani C.A.Kapourani@ed.ac.uk
See Also
scmet, scmet_differential,
scmet_hvf_lvf
Examples
# Extract
sce <- scmet_to_sce(Y = scmet_dt$Y, X = scmet_dt$X)
andreaskapou/scMET documentation built on Feb. 1, 2024, 10:46 a.m.
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| scmet_to_sce | R Documentation |
Convert from scmet to SingleCellExperiment object.
Description
Helper function that converts an scmet to SCE object. The
structure of the SCE object to store single cell methylation data is the
following. We create two assays, met storing methylated CpGs and total
storing total number of CpGs. Rows correspond to features and columns to
cells, similar to scRNA-seq convention. The rownames and colnames slots
should store the feature and cell names, respectively. Covariates X
that might explain variability in mean (methylation) should be stored
in metadata(rowData(sce)$X.
Usage
scmet_to_sce(Y, X = NULL)
Arguments
Y |
Methylation data in data.table format. |
X |
(Optional) Matrix of covariates. |
Value
An SCE object with the structure described above.
Author(s)
C.A.Kapourani C.A.Kapourani@ed.ac.uk
See Also
scmet, scmet_differential,
scmet_hvf_lvf
Examples
# Extract
sce <- scmet_to_sce(Y = scmet_dt$Y, X = scmet_dt$X)
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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