maketree: Generating dendrograms for the entire chromosome

Description Usage Arguments Value Author(s) Examples

View source: R/maketree.R

Description

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

Usage

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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

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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 28, 2017, 6:58 p.m.