Man pages for rliger
Linked Inference of Genomic Experimental Relationships
| alignFactors | Align factor loadings to get final integration |
| as.liger | Converting other classes of data to a liger object |
| as.ligerDataset | Converting other classes of data to a ligerDataset object |
| bmmc | liger object of bone marrow subsample data with RNA and ATAC... |
| calcAgreement | Calculate agreement metric after integration |
| calcAlignment | Calculate alignment metric after integration |
| calcARI | Calculate adjusted Rand index (ARI) by comparing two cluster... |
| calcDatasetSpecificity | Calculate a dataset-specificity score for each factor |
| calcNMI | Calculate Normalized Mutual Information (NMI) by comparing... |
| calcPurity | Calculate purity by comparing two cluster labeling variables |
| ccGeneHuman | Cell cycle gene set for human |
| centroidAlign | *[Experimental]* Align factor loading by centroid alignment... |
| closeAllH5 | Close all links (to HDF5 files) of a liger object |
| commandDiff | Check difference of two liger command |
| convertOldLiger | Convert old liger object to latest version |
| coordinate | Access ligerSpatialDataset coordinate data |
| createH5LigerDataset | Create on-disk ligerDataset Object |
| createLiger | Create liger object |
| createLigerDataset | Create in-memory ligerDataset object |
| deg.marker | Data frame for example marker DEG test result |
| deg.pw | Data frame for example pairwise DEG test result |
| dot-complexHeatmapDotPlot | Generate dot plot from input matrix with ComplexHeatmap |
| dot-ggCellViolin | Produce single violin plot with data frame passed from... |
| dot-ggplotLigerTheme | Generic ggplot theme setting for rliger package |
| dot-ggScatter | Produce single scatter plot with data frame passed from... |
| dot-plotHeatmap | General heatmap plotting with prepared matrix and data.frames |
| downsample | Downsample datasets |
| exportInteractTrack | Export predicted gene-pair interaction |
| factorGSEA | Test all factors for enrichment in a gene set |
| getFactorMarkers | Find shared and dataset-specific markers |
| getProportionMito | Calculate proportion mitochondrial contribution |
| H5Apply | Apply function to chunks of H5 data in ligerDataset object |
| importVignetteData | Import prepared dataset publically available |
| imputeKNN | Impute the peak counts from gene expression data referring to... |
| isH5Liger | Check if a liger or ligerDataset object is made of HDF5 file |
| is.newLiger | Check if given liger object if under new implementation |
| ligerATACDataset-class | Subclass of ligerDataset for ATAC modality |
| liger-class | liger class |
| ligerCommand-class | ligerCommand object: Record the input and time of a LIGER... |
| ligerDataset-class | ligerDataset class |
| liger-DEG | Find DEG between groups |
| ligerMethDataset-class | Subclass of ligerDataset for Methylation modality |
| ligerRNADataset-class | Subclass of ligerDataset for RNA 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 |
| 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 |
| mergeH5 | Merge hdf5 files |
| mergeSparseAll | Merge matrices while keeping the union of rows |
| modalOf | Return preset modality of a ligerDataset object or that of... |
| normalize | *[Deprecated]* Normalize raw counts data |
| 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 |
| pbmc | liger object of PBMC subsample data with Control and... |
| pbmcPlot | liger object of PBMC subsample data with plotting information... |
| peak | Access ligerATACDataset peak data |
| plotBarcodeRank | Create barcode-rank plot for each dataset |
| plotCellViolin | Generate violin/box 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 |
| plotDensityDimRed | Create density plot basing on specified coordinates |
| plotDimRed | Generate scatter plot(s) using liger object |
| plotEnhancedVolcano | Create volcano plot with EnhancedVolcano |
| plot.factorGSEA | GSEA plot for specific gene set and factor using factorGSEA... |
| plotGeneLoadings | Visualize factor expression and gene loading |
| plotGODot | Visualize GO enrichment test result in dot plot |
| plotGroupClusterDimRed | Comprehensive group splited cluster plot on dimension... |
| plotHeatmap | Plot Heatmap of Gene Expression or Factor Loading |
| plotMarkerHeatmap | Create heatmap for showing top marker expression in... |
| plotPairwiseDEGHeatmap | Create heatmap for pairwise DEG analysis result |
| plotProportion | Visualize proportion across two categorical variables |
| plotProportionBox | Box plot of cluster proportion in each dataset, grouped by... |
| plotSankey | Make Riverplot/Sankey diagram that shows label mapping across... |
| plotSpatial | Visualize a spatial dataset |
| plotVarFeatures | Plot the variance vs mean of feature expression |
| plotViolin | Visualize gene expression or cell metadata with violin plot |
| plotVolcano | Create volcano plot for Wilcoxon test result |
| print.factorGSEA | Show information about factorGSEA object |
| quantileAlignSNF | *[Superseded]* Quantile align (normalize) factor loadings |
| quantileNorm | Quantile Align (Normalize) Factor Loadings |
| quantile_norm-deprecated | *[Superseded]* Quantile align (normalize) factor loading |
| read10X | Load in data from 10X |
| read10XFiles | Read 10X cellranger files (matrix, barcodes and features)... |
| read10XH5 | Read 10X HDF5 file |
| readH5AD | Read matrix from H5AD file |
| readLiger | Read liger object from RDS file |
| readSubset | *[Superseded]* See 'downsample' |
| reexports | Objects exported from other packages |
| removeMissing | Remove missing cells or features from liger object |
| restoreH5Liger | Restore links (to HDF5 files) for reloaded liger/ligerDataset... |
| retrieveCellFeature | Retrieve a single matrix of cells from a slot |
| reverseMethData | Create "scaled data" for DNA methylation datasets |
| rliger-deprecated | Deprecated functions in package 'rliger'. |
| rliger-package | rliger: Linked Inference of Genomic Experimental... |
| runCINMF | 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... |
| runGSEA | Analyze biological interpretations of metagene |
| runINMF | Perform iNMF on scaled datasets |
| runIntegration | Integrate scaled datasets with iNMF or variant methods |
| runOnlineINMF | Perform online iNMF on scaled datasets |
| runTSNE | Perform t-SNE dimensionality reduction |
| runUINMF | Perform Mosaic iNMF (UINMF) on scaled datasets with unshared... |
| runUMAP | Perform UMAP Dimensionality Reduction |
| scaleNotCenter | Scale genes by root-mean-square across cells |
| selectBatchHVG | *[Experimental]* Batch-aware highly variable gene selection |
| selectGenes | Select a subset of informative genes |
| selectGenesVST | Select variable genes from one dataset with Seurat VST method |
| sub-liger | Subset liger with brackets |
| sub-ligerDataset | Subset ligerDataset object |
| subsetLiger | Subset liger object |
| subsetLigerDataset | Subset ligerDataset object |
| sub-sub-liger | Get cell metadata variable |
| suggestK | *[Experimental]* Suggest optimal K value for the... |
| summary.factorGSEA | Show significant results from factorGSEA |
| updateLigerObject | Update old liger object to up-to-date structure |
| writeH5 | Write in-memory data into H5 file |
| writeH5AD | Write liger object to H5AD files |
