Convenience Functions for Biscuit
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Documentation for package ‘biscuiteer’ version 1.23.0
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| biscuiteer-package | Convenience Functions for Biscuit |
| atRegions | Summarize a bsseq dataset over defined regions |
| binCoverage | Bin CpG or CpH coverage to simplify and improve CNA "sketching" |
| biscuiteer | Convenience Functions for Biscuit |
| biscuiteer-methods | bsseq class methods (VCF-centric) added by biscuiteer |
| biscuitMetadata | Biscuit metadata from VCF header |
| BSseq-methods | bsseq class methods (VCF-centric) added by biscuiteer |
| byChromArm | A simple parallization step |
| byExtremality | Choose loci or features by extremality |
| checkBiscuitBED | Inspect Biscuit VCF and BED files |
| clocks | clocks |
| condenseSampleNames | Simplify sample names for a bsseq object |
| coverage | bsseq class methods (VCF-centric) added by biscuiteer |
| CpGindex | Measure methylation status for PRCs or PMDs |
| ENSR_subset.hg19 | ENSR_subset data from hg19 genome |
| ENSR_subset.hg38 | ENSR_subset data from hg38 genome |
| extremality | Compute fraction of a Bernoulli variance |
| fexpit | Helper function: expanded expit |
| filterLoci | Filter loci with zero coverage |
| fixAge | Turn 'epigenetic clock' into actual age |
| fixed-method | bsseq class methods (VCF-centric) added by biscuiteer |
| fixNAs | Replace NAs with another value |
| flogit | Helper function: squeezed logit |
| geno-method | bsseq class methods (VCF-centric) added by biscuiteer |
| getBiscuitMetadata | Biscuit metadata from VCF header |
| getClock | Retrieve 'epigenetic clock' models |
| getLogitFracMeth | Helper function for compartment inference |
| getMvals | Helper function for compartment inference |
| GRCh37.chromArm | GRCh37.chromArm |
| GRCh38.chromArm | GRCh38.chromArm |
| grToSeg | Dump GRanges to segmented data data.frame |
| H9state23unmeth.hg19 | H9state23unmeth.hg19 |
| H9state23unmeth.hg38 | H9state23unmeth.hg38 |
| header | bsseq class methods (VCF-centric) added by biscuiteer |
| header-method | bsseq class methods (VCF-centric) added by biscuiteer |
| hg19.chromArm | hg19.chromArm |
| hg38.chromArm | hg38.chromArm |
| HMM_CpG_islands.hg19 | HMM_CpG_islands.hg19 |
| HMM_CpG_islands.hg38 | HMM_CpG_islands.hg38 |
| info-method | bsseq class methods (VCF-centric) added by biscuiteer |
| loadBiscuit | Read biscuit output into bsseq object |
| makeBSseq | Make an in-memory bsseq object from a biscuit BED |
| meta-method | bsseq class methods (VCF-centric) added by biscuiteer |
| readBiscuit | Read biscuit output into bsseq object |
| readEpibed | Read in and decode the RLE representation of the epibed format out of biscuit epiread |
| reference | bsseq class methods (VCF-centric) added by biscuiteer |
| RRBSeq | (e)RRBS settings for dmrseq |
| samples-method | bsseq class methods (VCF-centric) added by biscuiteer |
| segToGr | Import a segmentation file into GRanges object |
| seqinfo.hg19 | seqinfo.hg19 |
| seqinfo.hg38 | seqinfo.hg38 |
| seqinfo.mm10 | seqinfo.mm10 |
| simplifySampleNames | Simplify bsseq sample names |
| summarizeBsSeqOver | Summarize methylation over provided regions |
| tabixRetrieve | Read from tabix-indexed bed file to list objects |
| unionize | Combine bsseq objects together without losing information |
| WGBSage | Guess ages using Horvath-style 'clock' models |
| WGBSeq | Wrapper for WGBS settings for dmrseq |
| _PACKAGE | Convenience Functions for Biscuit |