evaluateCorrDecay: Evaluate the decay of correlation versus distance between...

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Evaluate the decay of correlation versus distance between features

Description

For pairs of features evaluate the physical distance and the correlation

Usage

evaluateCorrDecay(treeList, gr, chromArray = seqlevels(gr), verbose = TRUE)

Arguments

treeList	list of hclust objects
gr	GenomicRanges object corresponding to features clustered in treeList
chromArray	Use this only this set of chromosmes. Can substantially reduce memory usage
verbose	show progress

Value

a data.frame of distance and correlation value for all pairs of features already evalauted in treeList. Note that runOrderedClusteringGenome() that returns treeList only evalutes correlation between a specified number of adjacent peaks

Examples

library(GenomicRanges)
library(ggplot2)

data('decorateData')

# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation ) 

# Evaluate how correlation between features decays with distance
dfDist = evaluateCorrDecay( treeList, simLocation )

# make plot
plotCorrDecay( dfDist )

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.