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 |