| 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 |