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

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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