Package: rliger 2.1.0.9001
Yichen Wang
rliger: Linked Inference of Genomic Experimental Relationships
Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
Authors:
rliger_2.1.0.9001.tar.gz
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rliger.pdf |rliger.html✨
rliger/json (API)
NEWS
| # Install 'rliger' in R: |
| install.packages('rliger', repos = c('https://welch-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/welch-lab/liger/issues
- bmmc - Liger object of bone marrow subsample data with RNA and ATAC modality
- deg.marker - Data frame for example marker DEG test result
- deg.pw - Data frame for example pairwise DEG test result
- pbmc - Liger object of PBMC subsample data with Control and Stimulated datasets
- pbmcPlot - Liger object of PBMC subsample data with plotting information available
nonnegative-matrix-factorizationsingle-cell
Last updated 1 days agofrom:41144e884e. Checks:OK: 7 WARNING: 1 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win-x86_64 | OK | Nov 14 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-win-x86_64 | OK | Nov 14 2024 |
| R-4.4-mac-x86_64 | OK | Nov 14 2024 |
| R-4.4-mac-aarch64 | OK | Nov 14 2024 |
| R-4.3-win-x86_64 | OK | Nov 14 2024 |
| R-4.3-mac-x86_64 | OK | Nov 14 2024 |
| R-4.3-mac-aarch64 | ERROR | Nov 14 2024 |
Exports:%<>%%>%alignFactorsas.ligeras.ligerDatasetcalcAgreementcalcAlignmentcalcARIcalcDatasetSpecificitycalcNMIcalcPuritycellMetacellMeta<-centroidAligncloseAllH5commandDiffcommandsconvertOldLigercoordinatecoordinate<-createH5LigerDatasetcreateLigercreateLigerDatasetdatasetdataset<-datasetsdatasets<-defaultClusterdefaultCluster<-defaultDimReddefaultDimRed<-dimReddimRed<-dimRedsdimReds<-downsampleexportInteractTrackfeatureMetafeatureMeta<-getFactorMarkersgetH5FilegetMatrixgetProportionMitoh5fileInfoh5fileInfo<-importBMMCimportCGEimportPBMCimputeKNNis.newLigerisH5LigerligerATACDatasetligerCommandligerMethDatasetligerRNADatasetligerSpatialDatasetligerToSeuratlinkGenesAndPeakslouvainClustermakeFeatureMatrixmakeInteractTrackmakeRiverplotmapCellMetamergeDenseAllmergeH5mergeSparseAllmodalOfnormalizenormalizePeaknormDatanormData<-normPeaknormPeak<-online_iNMFoptimizeALSoptimizeNewDataoptimizeNewKoptimizeNewLambdaoptimizeSubsetplotBarcodeRankplotByDatasetAndClusterplotCellViolinplotClusterDimRedplotClusterFactorDotplotClusterGeneDotplotClusterGeneViolinplotClusterProportionsplotDatasetDimRedplotDensityDimRedplotDimRedplotEnhancedVolcanoplotFactorDimRedplotFactorHeatmapplotGeneDetectedViolinplotGeneDimRedplotGeneHeatmapplotGeneLoadingRankplotGeneLoadingsplotGeneViolinplotGODotplotGroupClusterDimRedplotMarkerHeatmapplotPairwiseDEGHeatmapplotPeakDimRedplotProportionplotProportionBarplotProportionBoxplotProportionDotplotProportionPieplotSankeyplotSpatial2DplotTotalCountViolinplotVarFeaturesplotVolcanoquantile_normquantileAlignSNFquantileNormrawDatarawData<-rawPeakrawPeak<-read10Xread10XATACread10XFilesread10XRNAreadLigerreadSubsetremoveMissingremoveMissingObsrestoreH5LigerrestoreOnlineLigerretrieveCellFeaturereverseMethDatarunCINMFrunClusterrunDoubletFinderrunGeneralQCrunGOEnrichrunGSEArunINMFrunIntegrationrunMarkerDEGrunOnlineINMFrunPairwiseDEGrunTSNErunUINMFrunUMAPrunWilcoxonscaleDatascaleData<-scaleNotCenterscaleUnsharedDatascaleUnsharedData<-selectGenesselectGenesVSTseuratToLigershowsubsetH5LigerDatasetsubsetLigersubsetLigerDatasetsubsetMemLigerDatasetupdateLigerObjectvarFeaturesvarFeatures<-varUnsharedFeaturesvarUnsharedFeatures<-writeH5
Dependencies:BHBiocGenericsbitbit64circlizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayondigestdoParalleldplyrdqrngfansifarverFNNforeachgenericsGetoptLongggplot2ggrepelGlobalOptionsgluegridExtragtablehdf5rigraphIRangesirlbaisobanditeratorslabelinglatticeleidenAlglifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepbmcapplypillarpkgconfigplyrpngpROCR6RANNRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressrjsonrlangRSpectraRtsneS4Vectorsscalessccoreshapesitmotibbletidyselectutf8uwotvctrsviridisviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate dot plot from input matrix with ComplexHeatmap | .complexHeatmapDotPlot |
| Produce single violin plot with data frame passed from upstream | .ggCellViolin |
| Generic ggplot theme setting for rliger package | .ggplotLigerTheme |
| Produce single scatter plot with data frame passed from upstream | .ggScatter |
| General heatmap plotting with prepared matrix and data.frames | .plotHeatmap |
| Align factor loadings to get final integration | alignFactors alignFactors.liger alignFactors.Seurat |
| Converting other classes of data to a liger object | as.liger as.liger.dgCMatrix as.liger.Seurat as.liger.SingleCellExperiment seuratToLiger |
| Converting other classes of data to a ligerDataset object | as.ligerDataset as.ligerDataset.default as.ligerDataset.ligerDataset as.ligerDataset.matrix as.ligerDataset.Seurat as.ligerDataset.SingleCellExperiment |
| liger object of bone marrow subsample data with RNA and ATAC modality | bmmc |
| Calculate agreement metric after integration | calcAgreement |
| Calculate alignment metric after integration | calcAlignment |
| Calculate adjusted Rand index (ARI) by comparing two cluster labeling variables | calcARI |
| Calculate a dataset-specificity score for each factor | calcDatasetSpecificity |
| Calculate Normalized Mutual Information (NMI) by comparing two cluster labeling variables | calcNMI |
| Calculate purity by comparing two cluster labeling variables | calcPurity |
| *[Experimental]* Align factor loading by centroid alignment (beta) | centroidAlign centroidAlign.liger centroidAlign.Seurat |
| Close all links (to HDF5 files) of a liger object | closeAllH5 closeAllH5.liger closeAllH5.ligerDataset |
| Check difference of two liger command | commandDiff |
| Convert old liger object to latest version | convertOldLiger |
| Access ligerSpatialDataset coordinate data | coordinate coordinate,liger,character-method coordinate,ligerSpatialDataset,missing-method coordinate<- coordinate<-,liger,character-method coordinate<-,ligerSpatialDataset,missing-method |
| Create on-disk ligerDataset Object | createH5LigerDataset |
| Create liger object | createLiger |
| Create in-memory ligerDataset object | createLigerDataset |
| Data frame for example marker DEG test result | deg.marker |
| Data frame for example pairwise DEG test result | deg.pw |
| Downsample datasets | downsample |
| Export predicted gene-pair interaction | exportInteractTrack |
| Find shared and dataset-specific markers | getFactorMarkers |
| Calculate proportion mitochondrial contribution | getProportionMito |
| Apply function to chunks of H5 data in ligerDataset object | H5Apply |
| Import prepared dataset publically available | importBMMC importCGE importPBMC |
| Impute the peak counts from gene expression data referring to an ATAC dataset after integration | imputeKNN |
| Check if given liger object if under new implementation | is.newLiger |
| Check if a liger or ligerDataset object is made of HDF5 file | isH5Liger |
| liger class | $.liger $<-.liger c.liger cellMeta cellMeta,liger,character-method cellMeta,liger,missing-method cellMeta,liger,NULL-method cellMeta<- cellMeta<-,liger,character-method cellMeta<-,liger,missing-method commands commands,liger-method dataset dataset,liger,character_OR_NULL-method dataset,liger,missing-method dataset,liger,numeric-method dataset<- dataset<-,liger,character,ANY,ANY,matrixLike-method dataset<-,liger,character,missing,ANY,ligerDataset-method dataset<-,liger,character,missing,ANY,NULL-method datasets datasets,liger-method datasets<- datasets<-,liger,logical-method datasets<-,liger,missing-method defaultCluster defaultCluster,liger-method defaultCluster<- defaultCluster<-,liger,ANY,ANY,character-method defaultCluster<-,liger,ANY,ANY,factor-method defaultCluster<-,liger,ANY,ANY,NULL-method defaultDimRed defaultDimRed,liger-method defaultDimRed<- defaultDimRed<-,liger,character-method dim,liger-method dimnames,liger-method dimnames<-,liger,list-method dimRed dimRed,liger,index-method dimRed,liger,missing_OR_NULL-method dimRed<- dimRed<-,liger,character,ANY,ANY,matrixLike-method dimRed<-,liger,index,ANY,ANY,NULL-method dimReds dimReds,liger-method dimReds<- dimReds<-,liger,list-method fortify.liger getH5File,liger,ANY-method getMatrix,liger,ANY,ANY,ANY-method length.liger lengths.liger liger liger-class names.liger names<-.liger normData,liger-method normData<-,liger,ANY,ANY,H5D-method normData<-,liger,ANY,ANY,matrixLike_OR_NULL-method rawData,liger-method rawData<-,liger,ANY,ANY,H5D-method rawData<-,liger,ANY,ANY,matrixLike_OR_NULL-method scaleData,liger,ANY-method scaleData<-,liger,ANY,ANY,H5D-method scaleData<-,liger,ANY,ANY,H5Group-method scaleData<-,liger,ANY,ANY,matrixLike_OR_NULL-method scaleUnsharedData,liger,character-method scaleUnsharedData,liger,numeric-method scaleUnsharedData<-,liger,ANY,ANY,H5D-method scaleUnsharedData<-,liger,ANY,ANY,H5Group-method scaleUnsharedData<-,liger,ANY,ANY,matrixLike_OR_NULL-method show,liger-method varFeatures varFeatures,liger-method varFeatures<- varFeatures<-,liger,ANY,character-method varUnsharedFeatures varUnsharedFeatures,liger,ANY-method varUnsharedFeatures,ligerDataset,missing-method varUnsharedFeatures<- varUnsharedFeatures<-,liger,ANY,ANY,character-method varUnsharedFeatures<-,ligerDataset,missing,ANY,character-method [[<-.liger |
| Subclass of ligerDataset for ATAC modality | ligerATACDataset ligerATACDataset-class |
| ligerCommand object: Record the input and time of a LIGER function call | ligerCommand ligerCommand-class show,ligerCommand-method |
| ligerDataset class | cbind.ligerDataset dim,ligerDataset-method dimnames,ligerDataset-method dimnames<-,ligerDataset,list-method featureMeta featureMeta,ligerDataset-method featureMeta<- featureMeta<-,ligerDataset-method getH5File getH5File,ligerDataset,missing-method getMatrix getMatrix,ligerATACDataset,ANY,missing,missing-method getMatrix,ligerDataset,ANY,missing,missing-method h5fileInfo h5fileInfo,ligerDataset-method h5fileInfo<- h5fileInfo<-,ligerDataset-method ligerDataset ligerDataset-class normData normData,ligerDataset-method normData<- normData<-,ligerDataset,ANY,ANY,H5D-method normData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method rawData rawData,ligerDataset-method rawData<- rawData<-,ligerDataset,ANY,ANY,H5D-method rawData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method scaleData scaleData,ligerDataset,missing-method scaleData<- scaleData<-,ligerDataset,ANY,ANY,H5D-method scaleData<-,ligerDataset,ANY,ANY,H5Group-method scaleData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method scaleUnsharedData scaleUnsharedData,ligerDataset,missing-method scaleUnsharedData<- scaleUnsharedData<-,ligerDataset,missing,ANY,H5D-method scaleUnsharedData<-,ligerDataset,missing,ANY,H5Group-method scaleUnsharedData<-,ligerDataset,missing,ANY,matrixLike_OR_NULL-method show,ligerDataset-method |
| Subclass of ligerDataset for Methylation modality | ligerMethDataset ligerMethDataset-class |
| Subclass of ligerDataset for RNA modality | ligerRNADataset ligerRNADataset-class |
| Subclass of ligerDataset for Spatial modality | ligerSpatialDataset ligerSpatialDataset-class |
| Convert between liger and Seurat object | ligerToSeurat |
| Linking genes to putative regulatory elements | linkGenesAndPeaks |
| *[Superseded]* Louvain algorithm for community detection | louvainCluster-deprecated |
| Fast calculation of feature count matrix | makeFeatureMatrix |
| *[Deprecated]* Export predicted gene-pair interaction | makeInteractTrack-deprecated |
| *[Deprecated]* Generate a river (Sankey) plot | makeRiverplot-deprecated |
| Create new variable from categories in cellMeta | mapCellMeta |
| Merge hdf5 files | mergeH5 |
| Merge matrices while keeping the union of rows | mergeDenseAll mergeSparseAll |
| Return preset modality of a ligerDataset object or that of all datasets in a liger object | modalOf |
| Normalize raw counts data | normalize normalize.dgCMatrix normalize.liger normalize.ligerDataset normalize.matrix normalize.Seurat normalizePeak |
| *[Deprecated]* Perform online iNMF on scaled datasets | online_iNMF-deprecated |
| *[Deprecated]* Perform iNMF on scaled datasets | optimizeALS-deprecated |
| Perform factorization for new data | optimizeNewData |
| Perform factorization for new value of k | optimizeNewK |
| Perform factorization for new lambda value | optimizeNewLambda |
| Perform factorization for subset of data | optimizeSubset |
| liger object of PBMC subsample data with Control and Stimulated datasets | pbmc |
| liger object of PBMC subsample data with plotting information available | pbmcPlot |
| Create barcode-rank plot for each dataset | plotBarcodeRank |
| Generate violin/box plot(s) using liger object | plotCellViolin |
| Make dot plot of factor loading in cell groups | plotClusterFactorDot |
| Make dot plot of gene expression in cell groups | plotClusterGeneDot |
| Create violin plot for multiple genes grouped by clusters | plotClusterGeneViolin |
| Create density plot basing on specified coordinates | plotDensityDimRed |
| Generate scatter plot(s) using liger object | plotByDatasetAndCluster plotClusterDimRed plotDatasetDimRed plotDimRed plotFactorDimRed plotGeneDimRed plotPeakDimRed |
| Create volcano plot with EnhancedVolcano | plotEnhancedVolcano |
| Plot Heatmap of Gene Expression or Factor Loading | plotFactorHeatmap plotGeneHeatmap |
| Visualize factor expression and gene loading | plotGeneLoadingRank plotGeneLoadings |
| Visualize gene expression or cell metadata with violin plot | plotGeneDetectedViolin plotGeneViolin plotTotalCountViolin |
| Visualize GO enrichment test result in dot plot | plotGODot |
| Comprehensive group splited cluster plot on dimension reduction with proportion | plotGroupClusterDimRed |
| Create heatmap for showing top marker expression in conditions | plotMarkerHeatmap |
| Create heatmap for pairwise DEG analysis result | plotPairwiseDEGHeatmap |
| Visualize proportion across two categorical variables | plotClusterProportions plotProportion plotProportionBar plotProportionDot plotProportionPie |
| Box plot of cluster proportion in each dataset, grouped by condition | plotProportionBox |
| Make Riverplot/Sankey diagram that shows label mapping across datasets | plotSankey |
| Visualize a spatial dataset | plotSpatial2D plotSpatial2D.liger plotSpatial2D.ligerSpatialDataset |
| Plot the variance vs mean of feature expression | plotVarFeatures |
| Create volcano plot for Wilcoxon test result | plotVolcano |
| *[Superseded]* Quantile align (normalize) factor loading | quantile_norm-deprecated |
| *[Superseded]* Quantile align (normalize) factor loadings | quantileAlignSNF |
| Quantile Align (Normalize) Factor Loadings | quantileNorm quantileNorm.liger quantileNorm.Seurat |
| Access ligerATACDataset peak data | normPeak normPeak,liger,character-method normPeak,ligerATACDataset,missing-method normPeak<- normPeak<-,liger,character-method normPeak<-,ligerATACDataset,missing-method rawPeak rawPeak,liger,character-method rawPeak,ligerATACDataset,missing-method rawPeak<- rawPeak<-,liger,character-method rawPeak<-,ligerATACDataset,missing-method |
| Load in data from 10X | read10X read10XATAC read10XRNA |
| Read 10X cellranger files (matrix, barcodes and features) into R session | read10XFiles |
| Read liger object from RDS file | readLiger |
| *[Superseded]* See 'downsample' | readSubset |
| Remove missing cells or features from liger object | removeMissing removeMissingObs |
| Restore links (to HDF5 files) for reloaded liger/ligerDataset object | restoreH5Liger restoreOnlineLiger |
| Retrieve a single matrix of cells from a slot | retrieveCellFeature |
| Create "scaled data" for DNA methylation datasets | reverseMethData |
| Perform consensus iNMF on scaled datasets | runCINMF runCINMF.liger runCINMF.Seurat |
| SNN Graph Based Community Detection | runCluster |
| Doublet detection with DoubletFinder | runDoubletFinder |
| General QC for liger object | runGeneralQC |
| Run Gene Ontology enrichment analysis on differentially expressed genes. | runGOEnrich |
| Analyze biological interpretations of metagene | runGSEA |
| Perform iNMF on scaled datasets | runINMF runINMF.liger runINMF.Seurat |
| Integrate scaled datasets with iNMF or variant methods | runIntegration runIntegration.liger runIntegration.Seurat |
| Perform online iNMF on scaled datasets | runOnlineINMF runOnlineINMF.liger runOnlineINMF.Seurat |
| Find DEG between groups | runMarkerDEG runPairwiseDEG runWilcoxon |
| Perform t-SNE dimensionality reduction | runTSNE |
| Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features | runUINMF runUINMF.liger |
| Perform UMAP Dimensionality Reduction | runUMAP |
| Scale genes by root-mean-square across cells | scaleNotCenter scaleNotCenter.dgCMatrix scaleNotCenter.liger scaleNotCenter.ligerDataset scaleNotCenter.ligerMethDataset scaleNotCenter.Seurat |
| Select a subset of informative genes | selectGenes selectGenes.liger selectGenes.Seurat |
| Select variable genes from one dataset with Seurat VST method | selectGenesVST |
| Subset liger with brackets | sub-liger [.liger |
| Subset ligerDataset object | sub-ligerDataset [.ligerDataset |
| Get cell metadata variable | sub-sub-liger [[.liger |
| Subset liger object | subsetLiger |
| Subset ligerDataset object | subsetH5LigerDataset subsetLigerDataset subsetMemLigerDataset |
| Update old liger object to up-to-date structure | updateLigerObject |
| Write in-memory data into H5 file | writeH5 writeH5.default writeH5.dgCMatrix writeH5.liger writeH5.ligerDataset |
