Example simulation data for hapFabia

Description

The data obtained by simulateForFabia in binary format.

Usage

1

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

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