Linked Inference of Genomic Experimental Relationships


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Documentation for package ‘rliger’ version 1.0.1

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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
calcNormLoadings Calculate loadings for each factor
calcPurity Calculate purity
convertOldLiger Convert older liger object into most current version (based on class definition)
createLiger Create a liger object.
ctrl dgCMatrix object of PBMC subsample data with Control and Stimulated datasets
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
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
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
stim dgCMatrix object of PBMC subsample data with Control and Stimulated datasets
subsetLiger Construct a liger object with a specified subset
suggestK Visually suggest appropiate k value
suggestLambda Visually suggest appropriate lambda value