Man pages for yanwu2014/chromfunks
Functions for Analyzing Chromatin Accessibility Data
| AddLinkCorrelations | Add correlations between region accessiblity and gene... |
| CalcDiffAccess | Compute differentially accessible peaks for each cluster |
| chromfunks-deprecated | Deprecated functions in package 'chromfunks'. |
| ChromRegionEnrich | Compute enrichment in each column of the chromatin... |
| extend_gr | Extend granges by buffer length |
| extractField | Extract the desired field from a delimited string |
| FilterConns | Reformat coaccessible peaks in list format |
| find_all_diff-deprecated | find_all_diff |
| FindCausalPeaks | Identify most impactful SNPs for a given trait/cell type... |
| FindCausalProb | Find the posterior probability score of causal peaks... |
| FindLinkedGenes | Find genes coaccessible with causal peaks for each... |
| FindNearbyGenes | Find all genes within specified distance of each genomic... |
| flattenMat | Flatten Matrix into a vector |
| formatCisTopicPeaks | Reformat rownames |
| geneAnno | Get gene body information from a human txdb object |
| GetBinCounts | Get binned counts matrix Adapted from the Cicero package... |
| getBulkDev | Compute deviations on a ATAC counts matrix |
| GetClusterAvg | Average counts matrix by cluster/cell type |
| getPseudobulk | Helper function for generating a pseudo-bulk matrix |
| GetRegionCounts | Build accessibility matrices for peaks overlapping list of... |
| granges2df | Convert gRanges to dataframe |
| granges2peak | Function for converting a granges object into a character... |
| hello | Hello, World! |
| ImportCausalSNPs | Import causal snp bed files |
| invertList | Inverts a list |
| invertListVector | Inverts a list of named numeric vectors |
| LogTFIDF | Compute the log TF-IDF transform for accessibility matrices... |
| MotifEnrich | Computes motif enrichment with a hypergeometric distribution |
| MotifRegionLinks | Link TFs to peaks using motifs |
| peak2df | Function for converting peak names into a dataframe |
| peak2granges | Function for converting peak names into a granges object |
| PlotNetwork | Visualize a TF - gene network using igraph |
| RegionChromVAR | Run chromVAR on a subset of peaks overlapping a list of... |
| RegionGeneLinks | Compute relationship between arbitrary regions and genes... |
| RegionOverlapList | Overlap genomic regions |
| RegionOverlapScores | Get overlaps between list of granges and granges in matrix... |
| simpleCap | Capitalize the first letter of every word in a string |
| SubsetLinks | Subset networks by TF, region, or gene. |
| TFGeneLinks | Link TFs to genes |
| TFRegionLinks | Link TFs to regions using motifs and correlations between TF... |
| TopDiffPeaks | Subset to top differentially accessible peaks for each... |
| top_diff_peaks-deprecated | top_diff_peaks |
| unflattenVec | Unflatten a vector into a matrix |
