Description Usage Arguments Value See Also
Count Density after Dithering and Dimensionality Reduction (CDaDaDR).
1 2 |
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. |
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 |
BRD, PlotBRD, DitherCounts, Barbouille::ASH2D
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