hapFabia (version 1.14.0)

simulateIBDsegmentsFabia: 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.

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)