| atRegions | summarize a bsseq dataset over defined regions (for e.g.... |
| bigWigsToSegs | wrapper fn to process large numbers of bigWig'ed CN... |
| binCoverage | bin CpG/CpH coverage to simplify & improve CNA "sketching"... |
| biscuiteer-methods | BSseq class methods (VCF-centric) added by biscuiteer... |
| biscuitMetadata | metadata about a Biscuit run using its vcfHeader metadata... |
| byChromArm | an idiotically simple parallelization step |
| byExtremality | choose loci or features by extremality (fraction of Bernoulli... |
| checkBiscuitBED | inspect Biscuit BED and/or VCF output to make sure all is as... |
| condenseSampleNames | simplify sampleNames for a bsseq object |
| correctBsSeqCoverage | tweaked version of TitanCNA's preprocessing |
| correctDepth | tweaked version of HMMcopy's GC bias and mappability function |
| CpGindex | Measure hypermethylation-at-PRCs-in-CGIs and... |
| extremality | compute the fraction of a Bernoulli variance achieved by a... |
| fexpit | Helper function: expanded expit |
| filterLoci | filter loci with zero coverage in one or more conditions |
| fixAge | project Horvath-type 'epigenetic clock' raw output onto... |
| fixNAs | play nice with BSseq's expectations about the M matrix |
| flogit | Helper function: squeezed logit |
| getClock | biscuiteer supports several "epigenetic clock" models. This... |
| getLogitFracMeth | helper function for compartment inference... |
| grToSeg | dump GRanges to .seg files |
| loadHDF5 | a simple local wrapper around... |
| makeBSseq | make an in-core BSseq object from a biscuit BED |
| plotSegs | plotting WGBScopy results (modified from HMMcopy) |
| read.biscuit | a bsseq loader for Biscuit output (BED-like format, 2 or 3... |
| RRBSeq | eRRBS settings appropriate to dmrseq |
| saveHDF5 | a simple local wrapper around... |
| segToGr | reverse a grToSeg... import a segmentation file |
| simplifySampleNames | Simplify bsseq sample names (usually VCF columns) |
| summarizeBsSeqOver | Pretty much what it says on the tin. |
| TN_WGBS_CNA | Matched tumor-normal coverage processing & segmentation |
| unionize | Smoosh BSseq objects together without losing information. |
| unionizeBSseq | Smoosh a couple of BSseq objects together, sensibly. |
| WGBSage | Guess ages using various Horvath-style (Genome Biology, 2012)... |
| WGBSeq | wrapper for WGBS settings appropriate to dmrseq |
| WGBSseg | Copy number segmentation of GC- & mapping-corrected WGBS... |
