clusteringKmeansNestedHclust: perform kmeans clustering on matrix rows and return reordered...

Description Usage Arguments Value Examples

View source: R/functions_signal_operations.R

Description

perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments clusters are sorted using hclust on centers the contents of each cluster are sorted using hclust

Usage

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clusteringKmeansNestedHclust(mat, nclust, seed = 0)

Arguments

mat

A wide format matrix

nclust

the number of clusters

seed

passed to set.seed() to allow reproducibility

Value

data.table with 2 columns of cluster info. id column corresponds with input matrix rownames and is sorted within each cluster using hierarchical clusering group column indicates cluster assignment

Examples

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dt = data.table::copy(CTCF_in_10a_profiles_dt)
mat = data.table::dcast(dt, id ~ sample + x, value.var = "y" )
rn = mat$id
mat = as.matrix(mat[,-1])
rownames(mat) = rn
clust_dt = clusteringKmeansNestedHclust(mat, nclust = 3)
dt = merge(dt, clust_dt)
dt$id = factor(dt$id, levels = clust_dt$id)
dt[order(id)]

jrboyd/seqsetvis documentation built on Oct. 14, 2018, 3:04 p.m.