moduleSearch: moduleSearch

In xinchoubiology/Rcppsva: Rcpp Integration Surrogate Variable Analysis

Description

cutreeDynamic is a dynamic clustering method borrowed from package dynamicTreeCut, and in this method, we will clustered our pre-clustered beta matrix and calculate out their co-regulation methylation regions

Usage

moduleSearch(beta.expr = NULL, cor.type = c("pearson", "spearman"),
  sim.type = c("S", "U"), method = c("average", "ward", "single",
  "complete"), deepSplit = 1, cutHeight = 0.9, minClusterSize = min(10,
  ncol(beta.expr)/2), pamStage = TRUE, pamRespectsDendro = TRUE,
  verbose = 2, ...)

Arguments

beta.expr	pre-clustered genome region for co-regulation methylation status
cor.type	correlation type for dissimilarity calculation; "pearson"(Default) and "spearman"
sim.type	similarity type for hierachical clustering; "signed"(Default) and "unsigned"
method	hierachical clustering method; c("average", "ward", "single", "complete")
deepSplit	[0,1,2,3,4]. Parameter in cutreeDynamic to control the sensitivity of module detection
cutHeight	h_max in DynamicTreeCut method
minClusterSize	c_min minimum size of each cluster
pamStage	Only used for method "hybrid" dynamicTreecut; If TRUE, the (PAM-like)stage will be performed
pamRespectsDendro	Logical
usebigmemory	use bigmemory or not

Details

based on WGCNA and Dynamic Tree Cut, clustering the DMRs Dynamic Tree cut method to determine co-methylation modules of different regions

Value

A list with following component: clusters a vector of cluster labels for all CpG regions dendrogram dendrogram of Rclusterpp.hclust

Author(s)

Xin Zhou [e-mail]

xinchoubiology/Rcppsva documentation built on May 4, 2019, 1:06 p.m.