adjclust is a package that provides methods to perform adjacency-constrained hierarchical agglomerative clustering. Adjacency-constrained hierarchical agglomerative clustering is hierarchical agglomerative clustering (HAC) in which each observation is associated to a position, and the clustering is constrained so as only adjacent clusters are merged. It is useful in bioinformatics (e.g. Genome Wide Association Studies or Hi-C data analysis).
adjclust provides three user level functions:
hicClust, which are briefly explained below.
You can install adjclust from github with:
# install.packages("devtools") devtools::install_github("pneuvial/adjclust")
adjClust performs adjacency-constrained HAC for standard and sparse, similarity and dissimilarity matrices and
Matrix::dsCMatrix are the supported sparse matrix classes. Let’s look at a basic example
library("adjclust") sim <- matrix(c(1.0, 0.5, 0.2, 0.1, 0.5, 1.0, 0.1, 0.2, 0.2, 0.1, 1.0, 0.6, 0.1, 0.2 ,0.6 ,1.0), nrow=4) h <- 3 fit <- adjClust(sim, "similarity", h) plot(fit)
The result is of class
chac. It can be plotted as a dendrogram (as shown above). Successive merge and heights of clustering can be obtained by
snpClust performs adjacency-constrained HAC for specific application of Genome Wide Association Studies (GWAS). A minimal example is given below. See GWAS Vignette for details.
library("snpStats") #> Loading required package: survival #> Loading required package: Matrix data("ld.example", package = "snpStats") geno <- ceph.1mb[, -316] ## drop one SNP leading to one missing LD value h <- 100 ld.ceph <- ld(geno, stats = "R.squared", depth = h) image(ld.ceph, lwd = 0)
fit <- snpClust(geno, stats = "R.squared", h = h) #> Warning in run.snpClust(x, h = h, stats = stats): Forcing the LD similarity to #> be smaller than or equal to 1 #> as(<dsTMatrix>, "dgTMatrix") is deprecated since Matrix 1.4-2; do as(., "generalMatrix") instead #> Note: 133 merges with non increasing heights. plot(fit) #> Warning in plot.chac(fit): #> Detected reversals in dendrogram: mode = 'corrected', 'within-disp' or 'total-disp' might be more relevant.
hicClust performs adjacency-constrained HAC for specific application of Hi-C data analysis. A minimal example is given below. See Hi-C Vignette for details.
load(system.file("extdata", "hic_imr90_40_XX.rda", package = "adjclust")) binned <- binningC(hic_imr90_40_XX, binsize = 5e5) #> Bin size 'xgi' =500488 [1x500488] #> Bin size 'ygi' =500488 [1x500488] mapC(binned) #> minrange= 104 - maxrange= 36776.8
fitB <- hicClust(binned) #> Note: 5 merges with non increasing heights. plot(fitB) #> Warning in plot.chac(fitB): #> Detected reversals in dendrogram: mode = 'corrected', 'within-disp' or 'total-disp' might be more relevant.
Version 0.4.0 of this package was completed by Shubham Chaturvedi as a part of the Google Summer of Code 2017 program.