hapRes: Example result of 'hapFabia'

In hapFabia: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Description

Results of a hapFabia call. List containing

1. mergedIBDsegmentList: an object of the class IBDsegmentList that contains the extracted IBD segments that were extracted from two histograms with different offset.

2. res: the result of FABIA.

3. sPF: samples per loading of this FABIA result.

4. annot: annotation for the genotype data.

5. IBDsegmentList1: an object of the class IBDsegmentList that contains the result of IBD segment extraction from the first histogram.

6. IBDsegmentList2: an object of the class IBDsegmentList that contains the result of IBD segment extraction from the second histogram.

7. mergedIBDsegmentList1: an object of the class IBDsegmentList that contains the merged result of the first IBD segment extraction (redundancies removed).

8. mergedIBDsegmentList2: an object of the class IBDsegmentList that contains the merged result of the second IBD segment extraction (redundancies removed).

Usage

hapRes

Format

List containing

1. mergedIBDsegmentList: an object of the class IBDsegmentList that contains the extracted IBD segments that were extracted from two histograms with different offset.

2. res: the result of FABIA.

3. sPF: samples per loading of this FABIA result.

4. annot: annotation for the genotype data.

5. IBDsegmentList1: an object of the class IBDsegmentList that contains the result of IBD segment extraction from the first histogram.

6. IBDsegmentList2: an object of the class IBDsegmentList that contains the result of IBD segment extraction from the second histogram.

7. mergedIBDsegmentList1: an object of the class IBDsegmentList that contains the merged result of the first IBD segment extraction (redundancies removed).

8. mergedIBDsegmentList2: an object of the class IBDsegmentList that contains the merged result of the second IBD segment extraction (redundancies removed).

Source

result of a call of hapFabia

References

S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.

See Also

IBDsegment-class, IBDsegmentList-class, analyzeIBDsegments, compareIBDsegmentLists, extractIBDsegments, findDenseRegions, hapFabia, hapFabiaVersion, hapRes, chr1ASW1000G, IBDsegmentList2excel, identifyDuplicates, iterateIntervals, makePipelineFile, matrixPlot, mergeIBDsegmentLists, mergedIBDsegmentList, plotIBDsegment, res, setAnnotation, setStatistics, sim, simu, simulateIBDsegmentsFabia, simulateIBDsegments, split_sparse_matrix, toolsFactorizationClass, vcftoFABIA

hapFabia documentation built on Nov. 8, 2020, 5:17 p.m.