SequenomMarkers: R wrapper script to run Sequenom Marker design pipeline

Description Usage Arguments Value Examples

View source: R/SequenomMarkers_v3.R

Description

SequenomMarkers runs the SNP genotyping marker design portion of the genotypeR pipeline.

This function designs Sequenom markers.

Usage

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SequenomMarkers(vcf1 = NULL, vcf2 = NULL, outdir = NULL,
  platform = "sq")

Arguments

vcf1

this is an uncompressed vcf file (Ref allele)

vcf2

this is an uncompressed vcf file (Alt allele)

outdir

this is where the tab-delimited extended bed file will be written

platform

is a character vector taking "sq" for sequenom (100 bp reference flanking region) or "gg" for goldengate (50 bp reference flanking region).

Value

SequenomMarker design into "outdir"

Examples

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## Not run: 
example_files <- system.file("SequenomMarkers_v2/two_sample/test_files", package = "genotypeR")

vcf1 <- paste(example_files, "Sample1.vcf", sep="/")
vcf2 <- paste(example_files, "Sample2.vcf", sep="/")

##look in outdir to look at the results in Master_SNPs.sorted.txt.
outdir <- paste(example_files, "test_dir", sep="/")

SequenomMarkers(vcf1, vcf2, outdir, platform="sq")


## End(Not run)

StevisonLab/genotypeR documentation built on May 27, 2018, 6:59 a.m.