CDaDaDR.2D: Density estimation in reduced dimensions

Description Usage Arguments Value See Also

View source: R/CDaDaDR_2D.R

Description

Count Density after Dithering and Dimensionality Reduction (CDaDaDR).

Usage

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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.