Multi-Assay Experiment with Spatial Context
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Documentation for package ‘MultiAssaySpatialExperiment’ version 0.99.12
Help Pages
-- A --
| addImg-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| aggregateByRegion | Aggregate assay values by shape region |
| aggregateByRegion-method | Aggregate assay values by shape region |
| annotateWithRegions | Annotate points with shape regions |
| annotateWithRegions-method | Annotate points with shape regions |
-- B --
| buildSpatialMap | Build a spatialMap table from sampleMap |
-- C --
| c-method | MultiAssaySpatialExperiment combining |
| cbind-method | MultiAssaySpatialExperiment combining |
| checkSpatialMap | Check spatialMap consistency |
| coerce-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| coerce-method | Spatial layer list objects |
-- G --
| getImg-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
-- I --
| imgData-method | MultiAssaySpatialExperiment objects |
| imgData<--method | MultiAssaySpatialExperiment objects |
| imgRaster-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| imgSource-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
-- L --
| labelsToShapes | Convert label rasters to polygon shapes |
-- M --
| mirrorImg-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| molecules-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| MultiAssaySpatialExperiment | MultiAssaySpatialExperiment objects |
| MultiAssaySpatialExperiment-class | MultiAssaySpatialExperiment objects |
| MultiAssaySpatialExperiment-combine | MultiAssaySpatialExperiment combining |
| MultiAssaySpatialExperiment-SpatialExperiment | MultiAssaySpatialExperiment - SpatialExperiment integration |
| MultiAssaySpatialExperiment-subset | MultiAssaySpatialExperiment subsetting |
-- P --
| PointsLayerList | Spatial layer list objects |
| PointsLayerList-class | Spatial layer list objects |
| prepMASE | Prepare components for a MultiAssaySpatialExperiment |
-- R --
| RasterLayerList | Spatial layer list objects |
| RasterLayerList-class | Spatial layer list objects |
| readCosMxMASE | Read NanoString CosMx SMI Spatial Data |
| readCSVForMASE | Read CSV Files for MASE |
| readCSVForMASE-method | Read CSV Files for MASE |
| readGeoJSONForMASE | Read GeoJSON Files for MASE |
| readGeoJSONForMASE-method | Read GeoJSON Files for MASE |
| readGeoParquetForMASE | Read GeoParquet Files for MASE |
| readGeoParquetForMASE-method | Read GeoParquet Files for MASE |
| readHDF5ForMASE | Read HDF5 Files for MASE |
| readHDF5ForMASE-method | Read HDF5 Files for MASE |
| readMERSCOPEMASE | Read Vizgen MERSCOPE Spatial Data |
| readParquetForMASE | Read Parquet Files for MASE |
| readParquetForMASE-method | Read Parquet Files for MASE |
| readVisiumHDMASE | Read 10x Genomics Visium HD Spatial Data |
| readVisiumMASE | Read 10x Genomics Visium Spatial Data |
| readXeniumMASE | Read 10x Genomics Xenium Spatial Data |
| rmvImg-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| rotateImg-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
-- S --
| scaleFactors-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| ShapesLayerList | Spatial layer list objects |
| ShapesLayerList-class | Spatial layer list objects |
| shapesToLabels | Rasterize polygon shapes to a label image |
| show-method | MultiAssaySpatialExperiment objects |
| show-method | Spatial layer list objects |
| spatial-accessors | Access spatial element slots |
| spatialCoords-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| spatialCoordsNames-method | MultiAssaySpatialExperiment - SpatialExperiment integration |
| spatialImage | Access spatial element slots |
| spatialImage-method | MultiAssaySpatialExperiment objects |
| spatialImage<- | Access spatial element slots |
| spatialImage<--method | MultiAssaySpatialExperiment objects |
| spatialImageNames | Access spatial element slots |
| spatialImageNames-method | MultiAssaySpatialExperiment objects |
| spatialImages | Access spatial element slots |
| spatialImages-method | MultiAssaySpatialExperiment objects |
| spatialImages<- | Access spatial element slots |
| spatialImages<--method | MultiAssaySpatialExperiment objects |
| spatialJoin | Spatial join between spatial layer tables |
| spatialJoin-method | Spatial join between spatial layer tables |
| spatialLabel | Access spatial element slots |
| spatialLabel-method | MultiAssaySpatialExperiment objects |
| spatialLabel<- | Access spatial element slots |
| spatialLabel<--method | MultiAssaySpatialExperiment objects |
| spatialLabelNames | Access spatial element slots |
| spatialLabelNames-method | MultiAssaySpatialExperiment objects |
| spatialLabels | Access spatial element slots |
| spatialLabels-method | MultiAssaySpatialExperiment objects |
| spatialLabels<- | Access spatial element slots |
| spatialLabels<--method | MultiAssaySpatialExperiment objects |
| SpatialLayerList-class | Spatial layer list objects |
| spatialMap | Access spatial element slots |
| spatialMap-method | MultiAssaySpatialExperiment objects |
| spatialMap<- | Access spatial element slots |
| spatialMap<--method | MultiAssaySpatialExperiment objects |
| spatialMatch | Spatial match for DataFrame |
| spatialMatch-method | Spatial match for DataFrame |
| spatialOverlaps | Spatial overlap predicate for DataFrame |
| spatialOverlaps-method | Spatial overlap predicate for DataFrame |
| spatialPoint | Access spatial element slots |
| spatialPoint-method | MultiAssaySpatialExperiment objects |
| spatialPoint<- | Access spatial element slots |
| spatialPoint<--method | MultiAssaySpatialExperiment objects |
| spatialPointNames | Access spatial element slots |
| spatialPointNames-method | MultiAssaySpatialExperiment objects |
| spatialPoints | Access spatial element slots |
| spatialPoints-method | MultiAssaySpatialExperiment objects |
| spatialPoints<- | Access spatial element slots |
| spatialPoints<--method | MultiAssaySpatialExperiment objects |
| spatialShape | Access spatial element slots |
| spatialShape-method | MultiAssaySpatialExperiment objects |
| spatialShape<- | Access spatial element slots |
| spatialShape<--method | MultiAssaySpatialExperiment objects |
| spatialShapeNames | Access spatial element slots |
| spatialShapeNames-method | MultiAssaySpatialExperiment objects |
| spatialShapes | Access spatial element slots |
| spatialShapes-method | MultiAssaySpatialExperiment objects |
| spatialShapes<- | Access spatial element slots |
| spatialShapes<--method | MultiAssaySpatialExperiment objects |
| subsetByAssay-method | MultiAssaySpatialExperiment subsetting |
| subsetByBoundingBox | MultiAssaySpatialExperiment subsetting |
| subsetByBoundingBox-method | MultiAssaySpatialExperiment subsetting |
| subsetByColData-method | MultiAssaySpatialExperiment subsetting |
| subsetByColumn-method | MultiAssaySpatialExperiment subsetting |
| subsetByPolygon | MultiAssaySpatialExperiment subsetting |
| subsetByPolygon-method | MultiAssaySpatialExperiment subsetting |
| subsetByRow-method | MultiAssaySpatialExperiment subsetting |
-- misc --
| [-method | MultiAssaySpatialExperiment subsetting |