simulateIBDsegmentsFabia: Generates simulated genotyping data with IBD segments for...

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

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.

Value

Generates simulated genotyping data with IBD segments for fabia

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)

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