getSampleDistance: getSampleDistance

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

View source: R/clustering.R

Description

Get distance between samples based on bias corrected deviations

Usage

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

Arguments

object

deviations result

threshold

threshold for variability

initial_dims

initial dimentions for preliminary dimensionality reduction via pca

distance_function

distance function to use

Details

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.

Value

dist object for distance between samples

Author(s)

Alicia Schep

See Also

getSampleCorrelation

Examples

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# 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!

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.