# Linked Inference of Genomic Experimental Relationships

## Documentation for package ‘rliger’ version 1.0.0

- DESCRIPTION file.

## Help Pages

calcAgreement | Calculate agreement metric
calcAlignment | Calculate alignment metric
calcAlignmentPerCluster | Calculate alignment for each cluster
calcARI | Calculate adjusted Rand index
calcDatasetSpecificity | Calculate a dataset-specificity score for each factor
calcGeneVars | Calculate variance of gene expression across cells in an online fashion
calcPurity | Calculate purity
convertOldLiger | Convert older liger object into most current version (based on class definition)
createLiger | Create a liger object.
getFactorMarkers | Find shared and dataset-specific markers
getGeneValues | Get gene expression values from list of expression matrices.
getProportionMito | Calculate proportion mitochondrial contribution
imputeKNN | Impute the query cell expression matrix
liger | The LIGER Class
liger-class | The LIGER Class
ligerToSeurat | Create a Seurat object containing the data from a liger object
linkGenesAndPeaks | Linking genes to putative regulatory elements
louvainCluster | Louvain algorithm for community detection
makeFeatureMatrix | Fast calculation of feature count matrix
makeInteractTrack | Export predicted gene-pair interaction
makeRiverplot | Generate a river (Sankey) plot
mergeH5 | Merge hdf5 files
nnzeroGroups | nnzeroGroups
nnzeroGroups.dgCMatrix | nnzeroGroups
nnzeroGroups.matrix | nnzeroGroups
nonneg | Perform thresholding on dense matrix
normalize | Normalize raw datasets to column sums
online_iNMF | Perform online iNMF on scaled datasets
optimizeALS | Perform iNMF on scaled datasets
optimizeALS.liger | Perform iNMF on scaled datasets
optimizeALS.list | 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
plotByDatasetAndCluster | Plot t-SNE coordinates of cells across datasets
plotClusterFactors | Plot heatmap of cluster/factor correspondence
plotClusterProportions | Plot cluster proportions by dataset
plotFactors | Plot scatter plots of unaligned and aligned factor loadings
plotFeature | Plot specific feature on t-SNE coordinates
plotGene | Plot gene expression on dimensional reduction (t-SNE) coordinates
plotGeneLoadings | Generate t-SNE plots and gene loading plots
plotGenes | Plot expression of multiple genes
plotGeneViolin | Plot violin plots for gene expression
plotWordClouds | Generate word clouds and t-SNE plots
quantileAlignSNF | Quantile align (normalize) factor loadings
quantile_norm | Quantile align (normalize) factor loadings
quantile_norm.liger | Quantile align (normalize) factor loadings
quantile_norm.list | Quantile align (normalize) factor loadings
rank_matrix | rank_matrix
rank_matrix.dgCMatrix | rank_matrix
rank_matrix.matrix | rank_matrix
read10X | Read 10X alignment data (including V3)
readSubset | Sample data for plotting
removeMissingObs | Remove cells/genes with no expression across any genes/cells
reorganizeLiger | Construct a liger object organized by another feature
restoreOnlineLiger | Restore links (to hdf5 files) for reloaded online Liger object
runGSEA | Analyze biological interpretations of metagene
runTSNE | Perform t-SNE dimensionality reduction
runUMAP | Perform UMAP dimensionality reduction
runWilcoxon | Perform Wilcoxon rank-sum test
scaleNotCenter | Scale genes by root-mean-square across cells
selectGenes | Select a subset of informative genes
seuratToLiger | Create liger object from one or more Seurat objects
show | show method for liger
show-method | show method for liger
subsetLiger | Construct a liger object with a specified subset
suggestK | Visually suggest appropiate k value
suggestLambda | Visually suggest appropriate lambda value
sumGroups | sumGroups
sumGroups.dgCMatrix | sumGroups
sumGroups.matrix | sumGroups