# Convenience Functions for Biscuit

## Documentation for package ‘biscuiteer’ version 1.25.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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