Description Usage Arguments Value Author(s) Examples
Calculate Baker's Gamma correlation coefficient between two trees
1 | snpcor(snpdata, snptree, trait.dend)
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snpdata |
SNP data downloaded from open source databases such as <http://msub.csbio.unc.edu/> or <http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=snpQF> |
snptree |
a list of dendrograms generated from snp data |
trait.dend |
a dendrogram generated from quantitative trait data |
a data frame of positions, snp chromosomal location, and correlation coefficient
Xingyao Chen
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | set.seed(1234) #simulate quantitative 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 traitbiome
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 correlation coefficient for micribiome dendrogram and each SNP dendrogram
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