CARD.imputation: Construct an enhanced spatial expression map on the...
In YingMa0107/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
View source: R/CARD.imputation.R
CARD.imputation R Documentation
Construct an enhanced spatial expression map on the unmeasured tissue locations
Description
Construct an enhanced spatial expression map on the unmeasured tissue locations
Usage
CARD.imputation(CARD_object, NumGrids, ineibor = 10, exclude = NULL)
Arguments
CARD_object
CARD Object with estimated cell type compositions on the original spatial resolved transcriptomics data.
NumGrids
Initial number of newly grided spatial locations. The final number of newly grided spatial locations will be lower than this value since the newly grided locations outside the shape of the tissue will be filtered
ineibor
Numeric, number of neighbors used in the imputation on newly grided spatial locations, default is 10.
exclude
Vector, the rownames of spatial location data on the original resolution that you want to exclude. This is to avoid the weird detection of the shape.
Value
Return CARD object with the refined cell type compositions estimated for newly grided spots and the refined predicted gene expression (normalized).
YingMa0107/CARD documentation built on Feb. 14, 2024, 12:23 p.m.
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View source: R/CARD.imputation.R
| CARD.imputation | R Documentation |
Construct an enhanced spatial expression map on the unmeasured tissue locations
Description
Construct an enhanced spatial expression map on the unmeasured tissue locations
Usage
CARD.imputation(CARD_object, NumGrids, ineibor = 10, exclude = NULL)
Arguments
CARD_object |
CARD Object with estimated cell type compositions on the original spatial resolved transcriptomics data. |
NumGrids |
Initial number of newly grided spatial locations. The final number of newly grided spatial locations will be lower than this value since the newly grided locations outside the shape of the tissue will be filtered |
ineibor |
Numeric, number of neighbors used in the imputation on newly grided spatial locations, default is 10. |
exclude |
Vector, the rownames of spatial location data on the original resolution that you want to exclude. This is to avoid the weird detection of the shape. |
Value
Return CARD object with the refined cell type compositions estimated for newly grided spots and the refined predicted gene expression (normalized).
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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