Description Usage Arguments Value Examples
SequenomMarkers
runs the SNP genotyping marker design
portion of the genotypeR pipeline.
This function designs Sequenom markers.
1 2 | SequenomMarkers(vcf1 = NULL, vcf2 = NULL, outdir = NULL,
platform = "sq")
|
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). |
SequenomMarker design into "outdir"
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## 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)
|
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