DeLorean (version 1.2.0)

seriation.find.orderings: Use seriation package to find good orderings

Description

Use seriation package to find good orderings

Usage

seriation.find.orderings(dl, .methods = c("TSP", "R2E", "HC", "GW", "OLO"),
  scaled = c("scaled", "unscaled"), dim.red = c("none", "pca", "kfa", "ica",
  "mds"), dims = geom.series(base = 2, max = min(8, nrow(dl$expr) - 1)),
  num.cores = default.num.cores(), num.tau.to.keep = default.num.cores())

Arguments

dl

de.lorean object

.methods

The seriation methods to apply

scaled

Whether to use the scaled and/or unscaled expression data

dim.red

Dimension reduction methods to apply

dims

Number of dimensions to reduce to

num.cores

Number of cores to use in parallel

num.tau.to.keep

How many initialisations to keep