Man pages for beyondpie/pureRUtils
Commonly used R functions with pure R codes
| addMatToSnap | Add bmat or gmat to snap |
| AnnoyBuildIndex | Build the annoy index Ref: Seurat |
| AnnoyNN | Run annoy Ref: Seurat |
| AnnoySearch | Search an Annoy approximate nearest neighbor index |
| ArchRPalettes | List of color palettes that can be used in plots |
| calOvlpScoreOld | Calculate overlap scores. Old function, not expored and... |
| checkArgsExistOrStop | Check if element in argument has no defination argument... |
| checkFileExistOrStop | Check if file/dir exist, if not, then stop |
| cleanOutfile | Prepare path for a new output file. |
| downSampleOnSnap | Down sample snap object based on a given cluster meta. |
| emptySnapEmbedding | Empty snap's embedding recorded in smat slot if it has. |
| emptySnapGraph | Empty snap's KNN graph if it has. |
| filterSnapBmat | Filter bmat removing common bins and those overlapped with... |
| getContinuousColors | Get continous color with linear interplotation |
| getCutoffFromShuffledBmat | Get enriched bin's percentage cutoff based on shuffledBmat. |
| getIsolatedGroup | Based on pval matrix, link the nodes without significant... |
| getMatchDataFrame | Select subset of rows of data.frame based on the order of... |
| getMultipleColors | Get multiple distinct colors using viridis package. |
| getOverlapMatrix | Calculate Overlap Score matrix for ATAC and RNA jointly... |
| getOverlapMatrixOld | Calculate Overlap Score matrix for ATAC and RNA jointly... |
| getPvalueOfNDiff.default | Get number of diff bins and the pvalue given two groups. |
| getPvalueOfNDiff.multiGroup | Get number of diff bins and the pvalue for any two groups |
| ggPoint | A ggplot-based dot plot wrapper function |
| grapes-or-or-grapes | OR of NULL. Ref: Seurat If the first element is not NULL,... |
| igraphModule2List | Transfer modules from igraph::components to a list. |
| integrateWithScRNASeq | Integration with single-cell RNA sequencing data |
| landmarkEmbedding | SnapATAC landmark embedding. |
| listOfNumeric2str | Transer list of numeric to string |
| loadRData | load RData file like readRDS |
| orderSnap | Order Snap based on the sample information This is critical... |
| paletteContinuous | Continuous Color Palette |
| paletteDiscrete | Optimized discrete color palette generation |
| plot2D | Generate list of ggplot figures of umap/tsne on the features... |
| plotConsensus | Consensus plot. |
| plotDotplot | Get Seurat dot plot for snap gmat. |
| plotFeatureSingle | plotFeatureSingle Allow the object can be a matrix of... |
| plotFeatureSingle.SnapATAC | plotFeatureSingle from SnapATAC package Allow the object can... |
| prepareOutdir | If dir does not exists, then create it. |
| prepareOutfile | If file does not exists, then prepare it. |
| queryEmbedding | SnapATAC query embedding. |
| runKNN | Run SnapATAC KNN. |
| runLeiden | Run Leiden Algorithm. |
| sampleBasedOnDepth2 | Sample index based on sequence depth defined by log10UMI... |
| shuffleBmat | Shuffle bmat in both row and column. |
| SnapATACPalette | The color palettes from SnapATAC |
| snapGmat2Seurat | Convert snap object to Seurat by gmat |
| splitSelect | Get the field-th column of each string splitted by given... |
| strToAdjmat | Transfer specific strings to adjacent matrix A typical string... |
| theme_ArchR | ggplot2 default theme for ArchR |
| uptri2str | Transfer the upper tri of a matrix to a string |
