# Genome Polarization via Diagnostic Index Expectation Maximization

## Documentation for package ‘diemr’ version 1.5.5

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

## Help Pages

brenthis | Dataset of Butterfly Genotypes
CheckDiemFormat | diem input file checker
diem | Diagnostic Index Expectation Maximisation
emPolarise | Polarises a marker
hybridIndex | Compute hybrid index from genotypes, files, or numeric values
importPolarized | Imports genomic data polarized according to the specification
ModelOfDiagnostic | Model of Diagnostic Marker Based on All Individual State Counts
myotis | Dataset of Modified Genotypes of Bats
pHetErrOnStateCount | Hybrid index, heterozygosity, error rate
plotDeFinetti | Plot the De Finetti Diagram for Polarized Genotypes
plotMarkerAxis | Add a Marker Axis with Chromosome Names to a Plot of Polarized Genotypes
plotPolarized | Plot Polarized Genotypes
rank2map | Convert SNP Ranks To Windows Corresponding to Mapping Distance
readIncludedSites | Read genomic sites from a BED-like file
smoothPolarizedGenotypes | Smooth Polarized Genotype States
sStateCount | Count states in a vector
testdata | Dataset of Fish Genotypes
variantSites | Identify Variant Sites in Genotype Files
vcf2diem | Convert vcf files to diem format