meanSmoother: Windowed mean smoother

In biobenkj/compartmap: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Windowed mean smoother

Description

TODO: farm out to C++ and test, at least when there are no NAs

Usage

meanSmoother(x, k = 1, iter = 2, na.rm = TRUE, delta = 0, w = NULL)

Arguments

x	Input data matrix: samples are columns, regions/loci are rows
k	Number of windows to use (default k=1, i.e., 3 windows)
iter	Number of iterations to smooth (default is 2)
na.rm	Whether to remove NAs prior to smoothing (TRUE)
delta	Convergence threshhold (overrides iter if > 0; default is 0)
w	Weights, if using any (NULL)

Value

 Smoothed data matrix

Examples

dummy <- matrix(rnorm(10000), ncol=25)
smooth.dummy <- meanSmoother(dummy)
smooth.dummy <- meanSmoother(dummy, iter=3) 
smooth.dummy <- meanSmoother(dummy, delta=1e-3) 

biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.