cluster.molecule: Hierarchical clustering of molecules

In DiffCorr: Analyzing and Visualizing Differential Correlation Networks in Biological Data

Description

Cluster molecules

Usage

cluster.molecule(data, method = "pearson", linkage = "average",
  absolute = FALSE)

Arguments

data	matrix or data frame
method	c("pearson", "spearman", "kendall", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski")
linkage	c("average", "ward", "single", "complete", "mcquitty", "median", "centroid")
absolute	if TRUE, then 1-|COR| else 1-COR, default is FALSE

Value

an object of class 'hclust'

Author(s)

Atsushi Fukushima

Examples

cluster.molecule(as.matrix(t(iris[,1:4])), "pearson", "average")

Example output

sh: 1: cannot create /dev/null: Permission denied
Loading required package: pcaMethods
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘pcaMethods’

The following object is masked from ‘package:stats’:

    loadings

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:BiocGenerics’:

    normalize, path, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: fdrtool
Loading required package: multtest

Call:
hclust(d = dist, method = linkage)

Cluster method   : average 
Number of objects: 4 

DiffCorr documentation built on May 2, 2019, 3:46 p.m.