# Predicting cell states and their variability in single-cell or spatial omics data

## Documentation for package ‘SVP’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L M N P R S misc

## -- A --

as_tbl_df | convert the square matrix to long tidy table

## -- C --

c-method | Gene Set Variation Analysis Experiment methods
cal_lisa_f1 | calculate the F1 value based on LISA result in the specified category.
cal_lisa_f1,SingleCellExperiment | calculate the F1 value based on LISA result in the specified category.
cal_lisa_f1-method | calculate the F1 value based on LISA result in the specified category.
CancerSEAEnsemble | The Gene List of Cancer Single-cell State Atlas (CancerSEA)
CancerSEASymbol | The Gene List of Cancer Single-cell State Atlas (CancerSEA)
CellCycle.Hs | the Cell Cycle gene set
cluster.assign | clusting and assign the label for each feature(specify the gene sets).
cluster.assign,SingleCellExperiment | clusting and assign the label for each feature(specify the gene sets).
cluster.assign,SVPExperiment | clusting and assign the label for each feature(specify the gene sets).
cluster.assign-method | clusting and assign the label for each feature(specify the gene sets).
coerce-method | The SVPExperiment class

## -- D --

data_CacerSEA | The Gene List of Cancer Single-cell State Atlas (CancerSEA)
data_CancerSEA | The Gene List of Cancer Single-cell State Atlas (CancerSEA)
data_CellCycle.Hs | the Cell Cycle gene set
data_hpda_spe_cell_dec | an example of result of runSGSA by extracting with gsvaExp
data_sceSubPbmc | a subset data of pbmck3 from SeuratData
data_SenMayo | A gene set identifies senescent cells and predicts senescence-associated pathways across tissues

## -- E --

extract_weight_adj | extract the cell adjacent matrix from spatial space or reduction space
extract_weight_adj,SingleCellExperiment | extract the cell adjacent matrix from spatial space or reduction space
extract_weight_adj-method | extract the cell adjacent matrix from spatial space or reduction space

## -- F --

fast_cor | Calculation of correlations and associated p-values
fscoreDf | features score matrix extract method
fscoreDf-method | features score matrix extract method
fscoreDf<- | features score matrix extract method
fscoreDf<--method | features score matrix extract method
fscoreDfNames | features score matrix extract method
fscoreDfNames-method | features score matrix extract method
fscoreDfNames<- | features score matrix extract method
fscoreDfNames<--method | features score matrix extract method
fscoreDfs | features score matrix extract method
fscoreDfs-method | features score matrix extract method
fscoreDfs<- | features score matrix extract method
fscoreDfs<--method | features score matrix extract method

## -- G --

gsvaExp | Gene Set Variation Analysis Experiment methods
gsvaExp-method | Gene Set Variation Analysis Experiment methods
gsvaExp<- | Gene Set Variation Analysis Experiment methods
gsvaExp<--method | Gene Set Variation Analysis Experiment methods
gsvaExpNames | Gene Set Variation Analysis Experiment methods
gsvaExpNames-method | Gene Set Variation Analysis Experiment methods
gsvaExpNames<- | Gene Set Variation Analysis Experiment methods
gsvaExpNames<--method | Gene Set Variation Analysis Experiment methods
gsvaExps | Gene Set Variation Analysis Experiment methods
gsvaExps-method | Gene Set Variation Analysis Experiment methods
gsvaExps<- | Gene Set Variation Analysis Experiment methods
gsvaExps<--method | Gene Set Variation Analysis Experiment methods

## -- H --

hpda_spe_cell_dec | an example of result of runSGSA by extracting with gsvaExp

## -- I --

imgData-method | Some accessor functions to get the internal slots of SVPExperiment
imgData<--method | Some accessor functions to get the internal slots of SVPExperiment

## -- L --

length-method | Gene Set Variation Analysis Experiment methods
LISAResult | LISAResult
LISAsce | convert LISA result to SVPExperiment.
LISAsce,SingleCellExperiment | convert LISA result to SVPExperiment.
LISAsce-method | convert LISA result to SVPExperiment.

## -- M --

mainGsvaExpName | Gene Set Variation Analysis Experiment methods
mainGsvaExpName-method | Gene Set Variation Analysis Experiment methods
mainGsvaExpName<- | Gene Set Variation Analysis Experiment methods
mainGsvaExpName<--method | Gene Set Variation Analysis Experiment methods
mob_marker_genes | the marker genes of mouse olfactory bulb
mob_sce | the single cell gene profiler of a mouse olfactory bulb

## -- N --

names-method | Gene Set Variation Analysis Experiment methods
names<--method | Gene Set Variation Analysis Experiment methods

## -- P --

plot_heatmap_globalbv | plot_heatmap_globalbv
pred.cell.signature | predict the cell signature according the gene sets or pathway activity score.
pred.cell.signature,SingleCellExperiment | predict the cell signature according the gene sets or pathway activity score.
pred.cell.signature,SVPExperiment | predict the cell signature according the gene sets or pathway activity score.
pred.cell.signature-method | predict the cell signature according the gene sets or pathway activity score.

## -- R --

runCORR | runCORR
runCORR,SingleCellExperiment | runCORR
runCORR,SVPExperiment | runCORR
runCORR-method | runCORR
runDetectMarker | Detecting the specific cell features with nearest distance of cells in MCA space
runDetectMarker,SingleCellExperiment | Detecting the specific cell features with nearest distance of cells in MCA space
runDetectMarker-method | Detecting the specific cell features with nearest distance of cells in MCA space
runDetectSVG | Detecting the spatially or single cell variable features with Moran's I or Geary's C
runDetectSVG,SingleCellExperiment | Detecting the spatially or single cell variable features with Moran's I or Geary's C
runDetectSVG,SVPExperiment | Detecting the spatially or single cell variable features with Moran's I or Geary's C
runDetectSVG-method | Detecting the spatially or single cell variable features with Moran's I or Geary's C
runENCODE | One hot encode for the specified cell category.
runENCODE,SingleCellExperiment | One hot encode for the specified cell category.
runENCODE-method | One hot encode for the specified cell category.
runGLOBALBV | Global Bivariate analysis for spatial autocorrelation
runGLOBALBV,SingleCellExperiment | Global Bivariate analysis for spatial autocorrelation
runGLOBALBV,SVPExperiment | Global Bivariate analysis for spatial autocorrelation
runGLOBALBV-method | Global Bivariate analysis for spatial autocorrelation
runKldSVG | Detecting the spatially or single cell variable features with Kullback–Leibler divergence of 2D weighted kernel density estimation
runKldSVG,SingleCellExperiment | Detecting the spatially or single cell variable features with Kullback–Leibler divergence of 2D weighted kernel density estimation
runKldSVG,SVPExperiment | Detecting the spatially or single cell variable features with Kullback–Leibler divergence of 2D weighted kernel density estimation
runKldSVG-method | Detecting the spatially or single cell variable features with Kullback–Leibler divergence of 2D weighted kernel density estimation
runLISA | Local indicators of spatial association analysis
runLISA,SingleCellExperiment | Local indicators of spatial association analysis
runLISA,SVPExperiment | Local indicators of spatial association analysis
runLISA-method | Local indicators of spatial association analysis
runLOCALBV | Local Bivariate analysis with spatial autocorrelation
runLOCALBV,SingleCellExperiment | Local Bivariate analysis with spatial autocorrelation
runLOCALBV,SVPExperiment | Local Bivariate analysis with spatial autocorrelation
runLOCALBV-method | Local Bivariate analysis with spatial autocorrelation
runMCA | Run Multiple Correspondence Analysis
runMCA,SingleCellExperiment | Run Multiple Correspondence Analysis
runMCA-method | Run Multiple Correspondence Analysis
runSGSA | Calculate the activity of gene sets in spatial or single-cell data with restart walk with restart and hyper test weighted.
runSGSA,SingleCellExperiment | Calculate the activity of gene sets in spatial or single-cell data with restart walk with restart and hyper test weighted.
runSGSA-method | Calculate the activity of gene sets in spatial or single-cell data with restart walk with restart and hyper test weighted.
runWKDE | Calculating the 2D Weighted Kernel Density Estimation
runWKDE,SingleCellExperiment | Calculating the 2D Weighted Kernel Density Estimation
runWKDE,SVPExperiment | Calculating the 2D Weighted Kernel Density Estimation
runWKDE-method | Calculating the 2D Weighted Kernel Density Estimation

## -- S --

sceSubPbmc | a subset data of pbmck3 from SeuratData
SenMayoSymbol | A gene set identifies senescent cells and predicts senescence-associated pathways across tissues
show-method | Some accessor functions to get the internal slots of SVPExperiment
spatialCoords-method | Some accessor functions to get the internal slots of SVPExperiment
spatialCoords<-,SVPExperiment | Some accessor functions to get the internal slots of SVPExperiment
spatialCoords<--method | Some accessor functions to get the internal slots of SVPExperiment
spatialCoordsNames-method | Some accessor functions to get the internal slots of SVPExperiment
spatialCoordsNames<--method | Some accessor functions to get the internal slots of SVPExperiment
svDf | spatial or single cell variable features matrix extract method
svDf-method | spatial or single cell variable features matrix extract method
svDf<- | spatial or single cell variable features matrix extract method
svDf<--method | spatial or single cell variable features matrix extract method
svDfNames | spatial or single cell variable features matrix extract method
svDfNames-method | spatial or single cell variable features matrix extract method
svDfNames<- | spatial or single cell variable features matrix extract method
svDfNames<--method | spatial or single cell variable features matrix extract method
svDfs | spatial or single cell variable features matrix extract method
svDfs-method | spatial or single cell variable features matrix extract method
svDfs<- | spatial or single cell variable features matrix extract method
svDfs<--method | spatial or single cell variable features matrix extract method
SVP-accessors | Some accessor functions to get the internal slots of SVPExperiment
SVPExperiment | The SVPExperiment class
SVPExperiment-class | The SVPExperiment class

## -- misc --

[-method | Gene Set Variation Analysis Experiment methods
[<--method | Gene Set Variation Analysis Experiment methods