Linked Inference of Genomic Experimental Relationships

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Documentation for package ‘rliger’ version 2.1.0

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

Help Pages

A B C D E F G H I L M N O P Q R S U V W misc

-- A --

alignFactors	Align factor loadings to get final integration
alignFactors.liger	Align factor loadings to get final integration
alignFactors.Seurat	Align factor loadings to get final integration
as.liger	Converting other classes of data to a liger object
as.liger.dgCMatrix	Converting other classes of data to a liger object
as.liger.Seurat	Converting other classes of data to a liger object
as.liger.SingleCellExperiment	Converting other classes of data to a liger object
as.ligerDataset	Converting other classes of data to a ligerDataset object
as.ligerDataset.default	Converting other classes of data to a ligerDataset object
as.ligerDataset.ligerDataset	Converting other classes of data to a ligerDataset object
as.ligerDataset.matrix	Converting other classes of data to a ligerDataset object
as.ligerDataset.Seurat	Converting other classes of data to a ligerDataset object
as.ligerDataset.SingleCellExperiment	Converting other classes of data to a ligerDataset object

-- B --

bmmc	liger object of bone marrow subsample data with RNA and ATAC modality

-- C --

c.liger	liger class
calcAgreement	Calculate agreement metric after integration
calcAlignment	Calculate alignment metric after integration
calcARI	Calculate adjusted Rand index (ARI) by comparing two cluster labeling variables
calcDatasetSpecificity	Calculate a dataset-specificity score for each factor
calcNMI	Calculate Normalized Mutual Information (NMI) by comparing two cluster labeling variables
calcPurity	Calculate purity by comparing two cluster labeling variables
cbind.ligerDataset	ligerDataset class
cellMeta	liger class
cellMeta-method	liger class
cellMeta<-	liger class
cellMeta<--method	liger class
centroidAlign	*[Experimental]* Align factor loading by centroid alignment (beta)
centroidAlign.liger	*[Experimental]* Align factor loading by centroid alignment (beta)
centroidAlign.Seurat	*[Experimental]* Align factor loading by centroid alignment (beta)
closeAllH5	Close all links (to HDF5 files) of a liger object
closeAllH5.liger	Close all links (to HDF5 files) of a liger object
closeAllH5.ligerDataset	Close all links (to HDF5 files) of a liger object
commandDiff	Check difference of two liger command
commands	liger class
commands-method	liger class
convertOldLiger	Convert old liger object to latest version
coordinate	Access ligerSpatialDataset coordinate data
coordinate-method	Access ligerSpatialDataset coordinate data
coordinate<-	Access ligerSpatialDataset coordinate data
coordinate<--method	Access ligerSpatialDataset coordinate data
createH5LigerDataset	Create on-disk ligerDataset Object
createLiger	Create liger object
createLigerDataset	Create in-memory ligerDataset object

-- D --

dataset	liger class
dataset-method	liger class
dataset<-	liger class
dataset<--method	liger class
datasets	liger class
datasets-method	liger class
datasets<-	liger class
datasets<--method	liger class
defaultCluster	liger class
defaultCluster-method	liger class
defaultCluster<-	liger class
defaultCluster<--method	liger class
defaultDimRed	liger class
defaultDimRed-method	liger class
defaultDimRed<-	liger class
defaultDimRed<--method	liger class
deg.marker	Data frame for example marker DEG test result
deg.pw	Data frame for example pairwise DEG test result
dim-method	liger class
dim-method	ligerDataset class
dimnames-method	liger class
dimnames-method	ligerDataset class
dimnames<--method	liger class
dimnames<--method	ligerDataset class
dimRed	liger class
dimRed-method	liger class
dimRed<-	liger class
dimRed<--method	liger class
dimReds	liger class
dimReds-method	liger class
dimReds<-	liger class
dimReds<--method	liger class
downsample	Downsample datasets

-- E --

exportInteractTrack

Export predicted gene-pair interaction

-- F --

featureMeta	ligerDataset class
featureMeta-method	ligerDataset class
featureMeta<-	ligerDataset class
featureMeta<--method	ligerDataset class
fortify.liger	liger class

-- G --

getFactorMarkers	Find shared and dataset-specific markers
getH5File	ligerDataset class
getH5File-method	liger class
getH5File-method	ligerDataset class
getMatrix	ligerDataset class
getMatrix-method	liger class
getMatrix-method	ligerDataset class
getProportionMito	Calculate proportion mitochondrial contribution

-- H --

H5Apply	Apply function to chunks of H5 data in ligerDataset object
h5fileInfo	ligerDataset class
h5fileInfo-method	ligerDataset class
h5fileInfo<-	ligerDataset class
h5fileInfo<--method	ligerDataset class

-- I --

importBMMC	Import prepared dataset publically available
importCGE	Import prepared dataset publically available
importPBMC	Import prepared dataset publically available
imputeKNN	Impute the peak counts from gene expression data referring to an ATAC dataset after integration
is.newLiger	Check if given liger object if under new implementation
isH5Liger	Check if a liger or ligerDataset object is made of HDF5 file

-- L --

length.liger	liger class
lengths.liger	liger class
liger	liger class
liger-class	liger class
ligerATACDataset	Subclass of ligerDataset for ATAC modality
ligerATACDataset-class	Subclass of ligerDataset for ATAC modality
ligerCommand	ligerCommand object: Record the input and time of a LIGER function call
ligerCommand-class	ligerCommand object: Record the input and time of a LIGER function call
ligerDataset	ligerDataset class
ligerDataset-class	ligerDataset class
ligerMethDataset	Subclass of ligerDataset for Methylation modality
ligerMethDataset-class	Subclass of ligerDataset for Methylation modality
ligerRNADataset	Subclass of ligerDataset for RNA modality
ligerRNADataset-class	Subclass of ligerDataset for RNA modality
ligerSpatialDataset	Subclass of ligerDataset for Spatial modality
ligerSpatialDataset-class	Subclass of ligerDataset for Spatial modality
ligerToSeurat	Convert between liger and Seurat object
linkGenesAndPeaks	Linking genes to putative regulatory elements
louvainCluster-deprecated	*[Superseded]* Louvain algorithm for community detection

-- M --

makeFeatureMatrix	Fast calculation of feature count matrix
makeInteractTrack-deprecated	*[Deprecated]* Export predicted gene-pair interaction
makeRiverplot-deprecated	*[Deprecated]* Generate a river (Sankey) plot
mapCellMeta	Create new variable from categories in cellMeta
mergeDenseAll	Merge matrices while keeping the union of rows
mergeH5	Merge hdf5 files
mergeSparseAll	Merge matrices while keeping the union of rows
modalOf	Return preset modality of a ligerDataset object or that of all datasets in a liger object

-- N --

names.liger	liger class
names<-.liger	liger class
normalize	Normalize raw counts data
normalize.dgCMatrix	Normalize raw counts data
normalize.liger	Normalize raw counts data
normalize.ligerDataset	Normalize raw counts data
normalize.matrix	Normalize raw counts data
normalize.Seurat	Normalize raw counts data
normalizePeak	Normalize raw counts data
normData	ligerDataset class
normData-method	liger class
normData-method	ligerDataset class
normData<-	ligerDataset class
normData<--method	liger class
normData<--method	ligerDataset class
normPeak	Access ligerATACDataset peak data
normPeak-method	Access ligerATACDataset peak data
normPeak<-	Access ligerATACDataset peak data
normPeak<--method	Access ligerATACDataset peak data

-- O --

online_iNMF-deprecated	*[Deprecated]* Perform online iNMF on scaled datasets
optimizeALS-deprecated	*[Deprecated]* Perform iNMF on scaled datasets
optimizeNewData	Perform factorization for new data
optimizeNewK	Perform factorization for new value of k
optimizeNewLambda	Perform factorization for new lambda value
optimizeSubset	Perform factorization for subset of data

-- P --

pbmc	liger object of PBMC subsample data with Control and Stimulated datasets
pbmcPlot	liger object of PBMC subsample data with plotting information available
plotBarcodeRank	Create barcode-rank plot for each dataset
plotByDatasetAndCluster	Generate scatter plot(s) using liger object
plotCellViolin	Generate violin/box plot(s) using liger object
plotClusterDimRed	Generate scatter plot(s) using liger object
plotClusterFactorDot	Make dot plot of factor loading in cell groups
plotClusterGeneDot	Make dot plot of gene expression in cell groups
plotClusterGeneViolin	Create violin plot for multiple genes grouped by clusters
plotClusterProportions	Visualize proportion across two categorical variables
plotDatasetDimRed	Generate scatter plot(s) using liger object
plotDensityDimRed	Create density plot basing on specified coordinates
plotDimRed	Generate scatter plot(s) using liger object
plotEnhancedVolcano	Create volcano plot with EnhancedVolcano
plotFactorDimRed	Generate scatter plot(s) using liger object
plotFactorHeatmap	Plot Heatmap of Gene Expression or Factor Loading
plotGeneDetectedViolin	Visualize gene expression or cell metadata with violin plot
plotGeneDimRed	Generate scatter plot(s) using liger object
plotGeneHeatmap	Plot Heatmap of Gene Expression or Factor Loading
plotGeneLoadingRank	Visualize factor expression and gene loading
plotGeneLoadings	Visualize factor expression and gene loading
plotGeneViolin	Visualize gene expression or cell metadata with violin plot
plotGODot	Visualize GO enrichment test result in dot plot
plotGroupClusterDimRed	Comprehensive group splited cluster plot on dimension reduction with proportion
plotMarkerHeatmap	Create heatmap for showing top marker expression in conditions
plotPairwiseDEGHeatmap	Create heatmap for pairwise DEG analysis result
plotPeakDimRed	Generate scatter plot(s) using liger object
plotProportion	Visualize proportion across two categorical variables
plotProportionBar	Visualize proportion across two categorical variables
plotProportionBox	Box plot of cluster proportion in each dataset, grouped by condition
plotProportionDot	Visualize proportion across two categorical variables
plotProportionPie	Visualize proportion across two categorical variables
plotSankey	Make Riverplot/Sankey diagram that shows label mapping across datasets
plotSpatial2D	Visualize a spatial dataset
plotSpatial2D.liger	Visualize a spatial dataset
plotSpatial2D.ligerSpatialDataset	Visualize a spatial dataset
plotTotalCountViolin	Visualize gene expression or cell metadata with violin plot
plotVarFeatures	Plot the variance vs mean of feature expression
plotVolcano	Create volcano plot for Wilcoxon test result

-- Q --

quantileAlignSNF	*[Superseded]* Quantile align (normalize) factor loadings
quantileNorm	Quantile Align (Normalize) Factor Loadings
quantileNorm.liger	Quantile Align (Normalize) Factor Loadings
quantileNorm.Seurat	Quantile Align (Normalize) Factor Loadings
quantile_norm-deprecated	*[Superseded]* Quantile align (normalize) factor loading

-- R --

rawData	ligerDataset class
rawData-method	liger class
rawData-method	ligerDataset class
rawData<-	ligerDataset class
rawData<--method	liger class
rawData<--method	ligerDataset class
rawPeak	Access ligerATACDataset peak data
rawPeak-method	Access ligerATACDataset peak data
rawPeak<-	Access ligerATACDataset peak data
rawPeak<--method	Access ligerATACDataset peak data
read10X	Load in data from 10X
read10XATAC	Load in data from 10X
read10XFiles	Read 10X cellranger files (matrix, barcodes and features) into R session
read10XRNA	Load in data from 10X
readLiger	Read liger object from RDS file
readSubset	*[Superseded]* See 'downsample'
removeMissing	Remove missing cells or features from liger object
removeMissingObs	Remove missing cells or features from liger object
restoreH5Liger	Restore links (to HDF5 files) for reloaded liger/ligerDataset object
restoreOnlineLiger	Restore links (to HDF5 files) for reloaded liger/ligerDataset object
retrieveCellFeature	Retrieve a single matrix of cells from a slot
reverseMethData	Create "scaled data" for DNA methylation datasets
runCINMF	Perform consensus iNMF on scaled datasets
runCINMF.liger	Perform consensus iNMF on scaled datasets
runCINMF.Seurat	Perform consensus iNMF on scaled datasets
runCluster	SNN Graph Based Community Detection
runDoubletFinder	Doublet detection with DoubletFinder
runGeneralQC	General QC for liger object
runGOEnrich	Run Gene Ontology enrichment analysis on differentially expressed genes.
runGSEA	Analyze biological interpretations of metagene
runINMF	Perform iNMF on scaled datasets
runINMF.liger	Perform iNMF on scaled datasets
runINMF.Seurat	Perform iNMF on scaled datasets
runIntegration	Integrate scaled datasets with iNMF or variant methods
runIntegration.liger	Integrate scaled datasets with iNMF or variant methods
runIntegration.Seurat	Integrate scaled datasets with iNMF or variant methods
runMarkerDEG	Find DEG between groups
runOnlineINMF	Perform online iNMF on scaled datasets
runOnlineINMF.liger	Perform online iNMF on scaled datasets
runOnlineINMF.Seurat	Perform online iNMF on scaled datasets
runPairwiseDEG	Find DEG between groups
runTSNE	Perform t-SNE dimensionality reduction
runUINMF	Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features
runUINMF.liger	Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features
runUMAP	Perform UMAP Dimensionality Reduction
runWilcoxon	Find DEG between groups

-- S --

scaleData	ligerDataset class
scaleData-method	liger class
scaleData-method	ligerDataset class
scaleData<-	ligerDataset class
scaleData<--method	liger class
scaleData<--method	ligerDataset class
scaleNotCenter	Scale genes by root-mean-square across cells
scaleNotCenter.dgCMatrix	Scale genes by root-mean-square across cells
scaleNotCenter.liger	Scale genes by root-mean-square across cells
scaleNotCenter.ligerDataset	Scale genes by root-mean-square across cells
scaleNotCenter.ligerMethDataset	Scale genes by root-mean-square across cells
scaleNotCenter.Seurat	Scale genes by root-mean-square across cells
scaleUnsharedData	ligerDataset class
scaleUnsharedData-method	liger class
scaleUnsharedData-method	ligerDataset class
scaleUnsharedData<-	ligerDataset class
scaleUnsharedData<--method	liger class
scaleUnsharedData<--method	ligerDataset class
selectGenes	Select a subset of informative genes
selectGenes.liger	Select a subset of informative genes
selectGenes.Seurat	Select a subset of informative genes
selectGenesVST	Select variable genes from one dataset with Seurat VST method
seuratToLiger	Converting other classes of data to a liger object
show-method	liger class
show-method	ligerCommand object: Record the input and time of a LIGER function call
show-method	ligerDataset class
sub-liger	Subset liger with brackets
sub-ligerDataset	Subset ligerDataset object
sub-sub-liger	Get cell metadata variable
subsetH5LigerDataset	Subset ligerDataset object
subsetLiger	Subset liger object
subsetLigerDataset	Subset ligerDataset object
subsetMemLigerDataset	Subset ligerDataset object

-- U --

updateLigerObject

Update old liger object to up-to-date structure

-- V --

varFeatures	liger class
varFeatures-method	liger class
varFeatures<-	liger class
varFeatures<--method	liger class
varUnsharedFeatures	liger class
varUnsharedFeatures-method	liger class
varUnsharedFeatures<-	liger class
varUnsharedFeatures<--method	liger class

-- W --

writeH5	Write in-memory data into H5 file
writeH5.default	Write in-memory data into H5 file
writeH5.dgCMatrix	Write in-memory data into H5 file
writeH5.liger	Write in-memory data into H5 file
writeH5.ligerDataset	Write in-memory data into H5 file

-- misc --

$.liger	liger class
$<-.liger	liger class
.complexHeatmapDotPlot	Generate dot plot from input matrix with ComplexHeatmap
.ggCellViolin	Produce single violin plot with data frame passed from upstream
.ggplotLigerTheme	Generic ggplot theme setting for rliger package
.ggScatter	Produce single scatter plot with data frame passed from upstream
.plotHeatmap	General heatmap plotting with prepared matrix and data.frames
[.liger	Subset liger with brackets
[.ligerDataset	Subset ligerDataset object
[[.liger	Get cell metadata variable
[[<-.liger	liger class