simu: Example simulation data for 'hapFabia'

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

Description

The data obtained by simulateForFabia in binary format.

Usage

simu

Format

contains a list simu with variables

1. namesL,

2. haploN,

3. snvs,

4. annot,

5. alleleIimp which contains the information on the implanted IBD segment: sample names, number of chromosomes/individuals, number of tagSNVs, annotation of tagSNVs, the genotype data where 0 = reference an 1 = minor allele.

annot is a list with entries:

1. chromosome,

2. position,

3. snvNames,

4. snvMajor,

5. snvMinor,

6. quality,

7. pass,

8. info,

9. fields,

10. frequency, and

11. changed.

Source

from simulateForFabia

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.