makePipelineFile {hapFabia} | R Documentation

## 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.

### 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)

[Package hapFabia version 1.29.0 Index]