illumina_Genotype_Table: Make genotypeR Alt_Ref_Table

Description Usage Arguments Value Examples

View source: R/illumina_Genotype_Table.R

Description

illumina_Genotype_Table produces the Alt_Ref_Table needed by initialize_genotypeR_data from illumina's goldengate platform.

Usage

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illumina_Genotype_Table(tab_delimited_file, flanking_region_length, chromosome)

Arguments

tab_delimited_file

is a tab delimited AB illumina GoldenGate file

flanking_region_length

is the length in bp of the flanking region of the SNP

chromosome

is a vector of chromosome names

Value

data frame useful used in genotypeR

Examples

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## Not run: 
##Files not included to provide working example
test_data <- read_in_illumina_GoldenGate(tab_delimited_file="path_to_goldengate_file"
, flanking_region_length=50, chromosome=rep("chr2",
length.out=length(552960)))
illumina_table <- illumina_Genotype_Table(tab_delimited_file= \
"path_to_goldengate_file", flanking_region_length=50,
chromosome=rep("chr2", length.out=length(552960)))

## End(Not run)

genotypeR documentation built on May 22, 2018, 5:07 p.m.