maketree: Generating dendrograms for the entire chromosome

In 16xchen/Biomy: Novel tool to find genetic factors that drive a set of traits

Description

Uses the finddistnace function to cluster strains based on dissimilarity of SNPs. One drendrogram for every 100 snps

Usage

maketree(snpdata, strain.names)

Arguments

snpdata	SNP data downloaded from opensource databases such as <http://msub.csbio.unc.edu/>or <http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=snpQF>
strain.names	a character vector of strain names

Value

a large list of dendrograms

Author(s)

Xingyao Chen

Examples

chrX = SampSNP() #load SNP data
strain.names=c(paste("strain", 1:(ncol(chrX)-1), sep="")) #assign strain names, strain names must match between trait and SNP dendrograms
mysnptree=maketree(snpdata=chrX, strain.names=strain.names)
mysnptree
plot(mysnptree[1])

16xchen/Biomy documentation built on May 5, 2019, 10:39 a.m.