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

In DeLorean: Estimates Pseudotimes for Single Cell Expression Data

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

DeLorean documentation built on May 2, 2019, 9:24 a.m.