GoldenGate2iCOM_design: Output GoldenGate markers for assay development with illumina...

In StevisonLab/genotypeR: SNP Genotype Marker Design and Analysis

Description

GoldenGate2iCOM_design outputs GoldenGate markers for SNP genotyping assay development with illumina iCOM.

Usage

GoldenGate2iCOM_design(SequenomMarkers, Target_Type = "SNP",
  Genome_Build_Version = "0", Chromosome = "0", Coordinate = "0",
  Source = "unknown", Source_Version = "0",
  Sequence_Orientation = "unknown", Plus_Minus = "Plus")

Arguments

SequenomMarkers	maker data frame from make SequenomMarkers
Target_Type	SNP/Indel
Genome_Build_Version	genome build version (number; default 0)
Chromosome	(default 0)
Coordinate	genomic coordinate (default 0)
Source	unknown/sequence information (default "unknown")
Source_Version	number (default 0)
Sequence_Orientation	"forward", "reverse", "unknown" (default "unknown")
Plus_Minus	strand orientation "Plus" or "Minus" (default "Plus")

Value

A data frame suited for the genotypeR package

Examples

library(genotypeR)
data(markers)
SequenomMarkers <- markers
##this is to reduce the marker lengths to 50 bp flanking SNP
SequenomMarkers$marker <- substr(markers$marker, 51, 155)
GG_SNPs <- GoldenGate2iCOM_design(SequenomMarkers)
write.csv(GG_SNPs, "test.csv", row.names=FALSE)

StevisonLab/genotypeR documentation built on May 5, 2019, 8 p.m.