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allgenesconsidered/example.R

Created December 12, 2017 18:56
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Generate dendrogram from samples
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example.R
library("SNPRelate")
snpgdsVCF2GDS(vcf.fn = "~/Desktop/dom_neg_genes_chr11_only/domneg_filtered_variants.vcf", out.fn = "~/Desktop/my.gds")
snpgdsSummary("~/Desktop/my.gds")
genofile <- openfn.gds("~/Desktop/my.gds")
ibs.hc <- snpgdsHCluster(snpgdsIBS(genofile, num.thread=2))
rv <- snpgdsCutTree(ibs.hc)
plot(rv$dendrogram, leaflab="textlike", main="DN Sample Clustering From Chr11 Varients")
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