# Linked Inference of Genomic Experimental Relationships

## Documentation for package ‘rliger’ version 2.2.1

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

## 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
ccGeneHuman | Cell cycle gene set for human
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 --

factorGSEA | Test all factors for enrichment in a gene set
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 | *[Deprecated]* Normalize raw counts data
normalize.DelayedArray | *[Deprecated]* Normalize raw counts data
normalize.dgCMatrix | *[Deprecated]* Normalize raw counts data
normalize.liger | *[Deprecated]* Normalize raw counts data
normalize.ligerDataset | *[Deprecated]* Normalize raw counts data
normalize.matrix | *[Deprecated]* Normalize raw counts data
normalize.Seurat | *[Deprecated]* Normalize raw counts data
normalizePeak | *[Deprecated]* 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
plot.factorGSEA | GSEA plot for specific gene set and factor using factorGSEA results
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
print.factorGSEA | Show information about factorGSEA object

## -- 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
read10XH5 | Read 10X HDF5 file
read10XH5Delay | Read 10X HDF5 file
read10XH5Mem | Read 10X HDF5 file
read10XRNA | Load in data from 10X
readH5AD | Read matrix from H5AD file
readH5ADDelay | Read matrix from H5AD file
readH5ADMem | Read matrix from H5AD file
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
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.DelayedArray | 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
selectBatchHVG | *[Experimental]* Batch-aware highly variable gene selection
selectBatchHVG.DelayedArray | *[Experimental]* Batch-aware highly variable gene selection
selectBatchHVG.dgCMatrix | *[Experimental]* Batch-aware highly variable gene selection
selectBatchHVG.liger | *[Experimental]* Batch-aware highly variable gene selection
selectBatchHVG.ligerDataset | *[Experimental]* Batch-aware highly variable gene selection
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
suggestK | *[Experimental]* Suggest optimal K value for the factorization
summary.factorGSEA | Show significant results from factorGSEA

## -- 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
writeH5AD | Write liger object to H5AD files
writeH5AD.dgCMatrix | Write liger object to H5AD files
writeH5AD.liger | Write liger object to H5AD files
writeH5AD.ligerDataset | Write liger object to H5AD files

## -- 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