makePipelineFile: Generate 'pipleline.R'

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

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.

Value

Run a whole IBD segment extraction pipeline

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())

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

setwd(old_dir)

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