hapFabia (version 1.14.0)

makePipelineFile: Generate pipleline.R

Description

makePipelineFile creates pipleline.R for sourcing with source("pipleline.R") to run a whole IBD segment extraction pipeline.

Usage

makePipelineFile(fileName,shiftSize=5000,intervalSize=10000,haplotypes=FALSE,dosage=FALSE)

Arguments

fileName

file name of the genotype file in vcf format

shiftSize

distance between start of adjacent intervals.

intervalSize

number of SNVs in a interval.

haplotypes

should haplotypes (phased genotypes) be used; default FALSE.

dosage

should dosages be used if haplotypes is FALSE; default FALSE.

Details

makePipelineFile creates Pipleline.R for sourcing with source("pipleline.R") to run a whole IBD segment extraction pipeline.

Attention: this code may run a while for large data sets.

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())

makePipelineFile(fileName="genotypeData",
   shiftSize=500,intervalSize=1000)
a <- scan(file = "pipeline.R",
   what = "character")
cat(a)

setwd(old_dir)