snpgdsHCluster: Hierarchical cluster analysis

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Hierarchical cluster analysis

Description

Perform hierarchical cluster analysis on the dissimilarity matrix.

Usage

snpgdsHCluster(dist, sample.id=NULL, need.mat=TRUE, hang=0.25)

Arguments

dist	an object of "snpgdsDissClass" from snpgdsDiss, an object of "snpgdsIBSClass" from snpgdsIBS, or a square matrix for dissimilarity
sample.id	to specify sample id, only work if dist is a matrix
need.mat	if TRUE, store the dissimilarity matrix in the result
hang	The fraction of the plot height by which labels should hang below the rest of the plot. A negative value will cause the labels to hang down from 0.

Details

Call the function hclust to perform hierarchical cluster analysis, using method="average".

Value

Return a list (class "snpgdsHCClass"):

sample.id	the sample ids used in the analysis
hclust	an object returned from hclust
dendrogram
dist	the dissimilarity matrix, if need.mat = TRUE

Author(s)

Xiuwen Zheng

See Also

snpgdsIBS, snpgdsDiss, snpgdsCutTree

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

pop.group <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
pop.group <- as.factor(pop.group)
pop.level <- levels(pop.group)

diss <- snpgdsDiss(genofile)
hc <- snpgdsHCluster(diss)
rv <- snpgdsCutTree(hc)
rv

# call 'plot' to draw a dendrogram
plot(rv$dendrogram, leaflab="none", main="HapMap Phase II")


# the distribution of Z scores
snpgdsDrawTree(rv, type="z-score", main="HapMap Phase II")

# draw dendrogram
snpgdsDrawTree(rv, main="HapMap Phase II",
    edgePar=list(col=rgb(0.5,0.5,0.5, 0.75), t.col="black"))


# close the file
snpgdsClose(genofile)

zhengxwen/SNPRelate documentation built on April 16, 2024, 8:42 a.m.