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

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

Get distance between samples based on bias corrected deviations

1 2	getSampleDistance(object, threshold = 1.5, initial_dims = 50, distance_function = dist)

`object`	deviations result
`threshold`	threshold for variability
`initial_dims`	initial dimentions for preliminary dimensionality reduction via pca
`distance_function`	distance function to use

This function will compute the distance between samples based on the normalized deviations. It will first remove correlated motifs / peak sets. Then the dimensionality will be further reduced via PCA if the number of dimensions exceeds initial_dims. Then the supplied distance_function will be used.

dist object for distance between samples

Alicia Schep

getSampleCorrelation

# Load very small example results from computeDeviations
data(mini_dev, package = "chromVAR")
sample_dist <- getSampleDistance(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  not meaningful!