drawtangle: Matching dendrograms

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

Description

Making tanglegrams of trait dendrograms matched up with snp dendrograms

Usage

drawtangle(snptree, trait.dend, indata, chr.num)

Arguments

snptree	A list of dendrograms generated from snp data
trait.dend	A dendrogram generated from quantitative trait data
indata	A dataframe similar to outputs by snocor or snpcor.best, that determines which SNP trees to plot out as tanglegrams.
chr.num	The chromosome number from which the snps are located

Value

Plots tanglegrams with the correlation value and the SNPs' location on chromosome in basepairs

Author(s)

Xingyao Chen

Examples

set.seed(1234) #simulate quantitatie trait dataframe
x <- rnorm(n=(16*12), mean=10, sd=30)
trait=matrix(x,16,12)
rname=paste("trait",1:16,sep="")
cname=paste("strain", 1:12, sep="")
rownames(trait)=rname
colnames(trait)=cname

mytrait.dend=traittree(traitdata=trait, nboot=10) #cluster strains by trait

chrX = SampSNP()  #load SNP data
strain.names=colnames(trait) #assign the same strain names
mysnptree=maketree(snpdata=chrX, strain.names=strain.names) #cluster strains by every 100 SNPs

mycordata=snpcor(snpdata=chrX, snptree=mysnptree, trait.dend=mytrait.dend) #calculate Baker's correlation coefficient for trait dendrogram and each SNP dendrogram
mycordata.best=snpcor.best(cordata=mycordata,threshold = 0.95) #find highly correlated SNP dendrograms
drawtangle(snptree=mysnptree, trait.dend=mytrait.dend, indata=mycordata.best, chr.num="X") #plot out as tanglegrams

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