# hapFabia: Identification of rare and short haplotypes in large sequencing data

## Documentation for package ‘hapFabia’ version 0.90.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

analyzeIBDs | analyzeIBDs: A loop over all extracted haplotype cluters or IBD tracts for descriptive statistics
compareIBDres | compareIBDres: Compare haplotype clusters or IBD tracts by hierarchical clustering
extractIBD | extractIBD: Find accumulations of values via histogram counts
getIBDs | getIBDs: Function to extract haplotype clusters / IBD tracts from 'fabia' results
hapFabia | hapFabia: Haplotype cluster extraction by FABIA
hapFabiaVersion | Display version info for package 'fabiaData'
hapRes | hapFabia Data: hapRes (result of 'hapFabia')
histL | histL: Histogram of the loadings of a 'fabia' result
ibd2excel | ibd2excel: Store haplotype cluster or IBD tract in EXCEL format
identifyDuplicates | identifyDuplicates: Identify duplicated haplotype clusters in different results
iterateSegments | iterateSegments: Loop over all segments which calls 'hapFabia'
makePipelineFile | makePipelineFile: Make 'Pipleline.R' for 'source("Pipleline.R")'
mergedIBD | hapFabia Data: mergedIBD (haplotype clusters found by 'hapFabia')
mergeIBDres | mergeIBDres: Merging and combining haplotype clusters or IBD tracts
plotIBDs | plotIBDs: Plot all haplotype clusters or IBD tracts of a list
plotL | plotL: Plot the loadings of a 'fabia' result
plotOneIBD | plotOneIBD: Plots a single haplotype cluster or IBD tract
plotRangeL | plotRangeL: Plot a haplotype cluster given samples, tagSNVs, and their physical positions
res | hapFabia Data: res (result of 'spfabia')
sim | sim: Similarity measure for haplotype cluster tagSNVs or individuals
simu | hapFabia Data: simulation (simulation data for 'hapFabia')
simulateForFabia | simulateForFabia: Constructs simulation data with rare variants and implanted haplotype clusters for 'fabia'
simulateHaplotypes | simulateHaplotypes: Constructs simulation data with rare variants and implanted haplotype clusters
snpPlot | snpPlot: Basic plot function for haplotype clusters and IBD tracts
split_sparse_matrix | split_sparse_matrix: Split genotype data in sparse matrix format into segments
topLZ | topLZ: Supply largest L or Z indexes/values of a 'fabia' result
vcftoFABIA | vcftoFABIA: Converting from vcf to sparse matrix format