A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.
|Author||Sepp Hochreiter <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Sepp Hochreiter <email@example.com>|
|License||LGPL (>= 2.1)|
analyzeIBDsegments: Loop over extracted IBD segments to supply a descriptive...
chr1ASW1000G: Example genotype data in 'vcf' format
compareIBDsegmentLists: Hierarchical clustering of IBD segments stored in IBD segment...
extractIBDsegments: Extract IBD segments from a 'fabia' result
findDenseRegions: Find accumulations of values via histogram counts
hapFabia: IBD segment extraction by FABIA
hapFabiaVersion: Display version info for package 'hapFabia'
hapRes: Example result of 'hapFabia'
IBDsegment-class: IBDsegment instances and methods
IBDsegmentList2excel: Store an IBD segment list in EXCEL / csv format
IBDsegmentList-class: IBDsegmentList instances and methods
identifyDuplicates: Identify duplicates of IBD segments
iterateIntervals: Loop over DNA intervals with a call of 'hapFabia'
makePipelineFile: Generate 'pipleline.R'
matrixPlot: Basic plot function for IBD segments
mergedIBDsegmentList: Example IBD segment list as a result of 'hapFabia'
mergeIBDsegmentLists: Merging IBD segments
plotIBDsegment: Plots an IBD segment given genotype data and tagSNVs
res: Example result of 'spfabia'
setAnnotation: Fills in annotations of tagSNVs of a list of IBD segments
setStatistics: Computes and stores the statistics of an IBD segment list
sim: Similarity measures for IBD segments
simu: Example simulation data for 'hapFabia'
simulateIBDsegments: Generates simulated genotyping data with IBD segments
simulateIBDsegmentsFabia: Generates simulated genotyping data with IBD segments for...
split_sparse_matrix: Splits genotyping data in sparse matrix format into intervals
toolsFactorizationClass: Tools to analyze results of 'fabia'
vcftoFABIA: Converting genotyping data from 'vcf' to sparse matrix format