getSampleCorrelation: getSampleCorrelation

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/clustering.R

Description

Get correlation between samples based on bias corrected deviations

Usage

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getSampleCorrelation(object, threshold = 1.5)

Arguments

object

deviations result

threshold

threshold for variability

Details

This function will compute the correlation between samples based on the normalized deviations. It will first remove correlated motifs/peak sets. Then the pearson correlation coefficient will be computed and returned.

Value

correlation matrix between samples

Author(s)

Alicia Schep

See Also

getSampleDistance

Examples

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# Load very small example results from computeDeviations
data(mini_dev, package = "chromVAR")
sample_cor <- getSampleCorrelation(mini_dev, threshold = 0.8)  
# setting very low variabilitiy threshold because this is mini data set
# threshold should generally be above 1
# Use plotVariability to get a sense of an appropriate threshold
# As this is mini data set, results probably not meaningful!

GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.