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

Description Usage Arguments Value Examples

View source: R/evaluateCorrDecay.R

Description

For pairs of features evaluate the physical distance and the correlation

Usage

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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

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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 July 26, 2021, 12:18 a.m.