getSampleCorrelation: getSampleCorrelation
In GreenleafLab/chromVAR: Chromatin Variation Across Regions

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

Get correlation between samples based on bias corrected deviations

1	getSampleCorrelation(object, threshold = 1.5)

`object`	deviations result
`threshold`	threshold for variability

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.

correlation matrix between samples

Alicia Schep

getSampleDistance

# 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!