Man pages for rliger
Linked Inference of Genomic Experimental Relationships
| 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... |
| calcNormLoadings | Calculate loadings for each factor |
| calcPurity | Calculate purity |
| convertOldLiger | Convert older liger object into most current version (based... |
| 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-class | The LIGER Class |
| liger-demodata | dgCMatrix object of PBMC subsample data with Control and... |
| ligerToSeurat | Create a Seurat object containing the data from a liger... |
| 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 |
| 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)... |
| 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 |
| 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... |
| 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-methods | 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 |
