Description Usage Arguments Value Author(s) Examples
Subsets dataframe from snpcor function to contain only the highly correlated SNP dendrograms
1 | snpcor.best(cordata, threshold)
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cordata |
q dataframe generated from the function snpcor |
threshold |
percent threshold (0-1) to search for highest correlations, default is 0.95 |
a subsetted correlation dataframe
Xingyao Chen
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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
mycordata.best=snpcor.best(cordata=mycordata,threshold = 0.95) #find highly correlated SNP dendrograms
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