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


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Documentation for package ‘hapFabia’ version 0.90.0

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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