simulateIBDsegmentsFabia {hapFabia} | R Documentation

## Generates simulated genotyping data with IBD segments for fabia

### Description

`simulateIBDsegmentsFabia`: R implementation of `simulateIBDsegmentsFabia`.

Genotype data is simulated which contains rare variants and implanted IBD segments. Output is written for the bicluster algorithm fabia.

### Usage

    simulateIBDsegmentsFabia(fileprefix="dataSim",
       minruns=1,maxruns=1,snvs=1000,individualsN=100,
       avDistSnvs=100,avDistMinor=10,noImplanted=1,
       implanted=10,length=50,minors=30,mismatches=0,
       mismatchImplanted=0.5,overlap=50)

### Arguments

`fileprefix` | prefix of file names containing data generated in this simulation.
`minruns` | start index for generating multiple data sets.
`maxruns` | end index for generating multiple data sets.
`snvs` | number of SNVs in this simulation.
`individualsN` | number of individuals in this simulation.
`avDistSnvs` | average genomic distance in bases between SNVs.
`avDistMinor` | average distance between minor alleles, thus `1/avDistMinor` is the average minor allele frequency (MAF).
`noImplanted` | number of IBD segments that are implanted.
`implanted` | number of individuals into which a specific IBD segment is implanted.
`length` | length of the IBD segments in number of SNVs.
`minors` | number of tagSNVs for each IBD segment.
`mismatches` | number of base mismatches of an implanted IBD segment to the original IBD segment.
`mismatchImplanted` | percentage of IBD segment occurrence that have mismatches.
`overlap` | minimal IBD segment overlap between implanted IBD segments (they are broken at the ends).

### Details

Data simulations for fabia focuses on rare variants but common variants are possible. Linkage disequilibrium and haplotype blocks are not simulated except by implanting IBD segments.

Simulated data is written to "...fabia_individuals.txt", "...fabia_annot.txt" "...fabia_mat.txt".

Implementation in R.

### Author(s)

Sepp Hochreiter

### 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`

### Examples

    old_dir <- getwd()
    setwd(tempdir())

    simulateIBDsegmentsFabia()

    setwd(old_dir)

[Package hapFabia version 1.22.0 Index]