getSampleCorrelation {chromVAR}R Documentation

getSampleCorrelation

Description

Get correlation between samples based on bias corrected deviations

Usage

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

# 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!

[Package chromVAR version 1.15.0 Index]