nb_clust: Netboost clustering step

In netboost: Network Analysis Supported by Boosting

Description

Netboost clustering step

Usage

nb_clust(filter, dist, datan, max_singleton = dim(datan)[2],
  min_cluster_size = 2L, ME_diss_thres = 0.25,
  cores = getOption("mc.cores", 2L), qc_plot = TRUE, n_pc = 1,
  robust_PCs = FALSE, nb_min_varExpl = 0.5, method = c("pearson",
  "kendall", "spearman"))

Arguments

filter	Filter-Matrix as generated by the nb_filter function.
dist	Distance-Matrix as generated by the nb_dist function.
datan	Data frame were rows correspond to samples and columns to features.
max_singleton	Integer. The maximal singleton in the clustering. Usually equals the number of features.
min_cluster_size	Integer. The minimum number of features in one module.
ME_diss_thres	Numeric. Module Eigengene Dissimilarity Threshold for merging close modules.
cores	Integer. Amount of CPU cores used (<=1 : sequential)
qc_plot	Logical. Create plot.
n_pc	Number of principal components and variance explained entries to be calculated. The number of returned variance explained entries is currently ‘min(n_pc,10)’. If given ‘n_pc’ is greater than 10, a warning is issued.
robust_PCs	Should PCA be calculated on ranked data (Spearman PCA)? Rotations will not correspond to original data if this is applied.
nb_min_varExpl	Minimum proportion of variance explained for returned module eigengenes. The number of PCs is capped at n_pc.
method	A character string specifying the method to be used for correlation coefficients.

Value

List

Examples

 data('tcga_aml_meth_rna_chr18',  package='netboost')
 cores <- as.integer(getOption('mc.cores', 2))
 datan <- as.data.frame(scale(tcga_aml_meth_rna_chr18, center=TRUE, 
 scale=TRUE))
 filter <- nb_filter(datan=datan, stepno=20L, until=0L, progress=1000L,
 cores=cores,mode=2L)
 dist <- nb_dist(datan=datan, filter=filter, soft_power=3L, cores=cores)
 max_singleton = dim(tcga_aml_meth_rna_chr18)[2]
 pdf("test.pdf",width=30)
 sum_res <- nb_clust(filter=filter, dist=dist, datan=datan,
 max_singleton=max_singleton, min_cluster_size=10L, ME_diss_thres=0.25,
 cores=cores, qc_plot=TRUE, n_pc=2L, nb_min_varExpl=0.5)
 dev.off()

netboost documentation built on Nov. 8, 2020, 4:58 p.m.