SequenomMarkers: R wrapper script to run Sequenom Marker design pipeline

In StevisonLab/genotypeR: SNP Genotype Marker Design and Analysis

Description

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

This function designs Sequenom markers.

Usage

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

## 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 5, 2019, 8 p.m.