CDaDaDR.2D: Density estimation in reduced dimensions

In benja0x40/Tightrope: ChIP-seq normalization according to background reads density

Description

Count Density after Dithering and Dimensionality Reduction (CDaDaDR).

Usage

CDaDaDR.2D(cnt, movs = NULL, bins = NULL, smoothing = NULL,
  dither = NULL, zscore = NULL, method = c("pca", "ica"))

Arguments

cnt	matrix of read counts (rows = observations, columns = measurement conditions).
movs	precomputed mean count values to be subtracted to each observation (default = NULL, zero).
bins	number of bins per principal component for density estimations (default = 500).
smoothing	number of consecutive bins for local average smoothing of estimated densities (default = 10).
dither	number of replicates of the count dithering performed by DitherCounts: 1 = single, 2 = duplicate, 3 = triplicate, etc. (default = 5).
zscore	transform read count projections into z-scores (default = TRUE, recommended).
method	projection method, either "pca" (default) performed by prcomp, or "ica" performed by icafast.

Value

CDaDaDR.2D returns a list with the following elements:

parameters	list with the value of each CDaDaDR.2D argument
status	list with informations on the dimensionality reduction
density	estimated density at each observation
projection	transformed count matrix

See Also

BRD, PlotBRD, DitherCounts, Barbouille::ASH2D

benja0x40/Tightrope documentation built on May 24, 2019, 1:35 a.m.