moduleTestAlongTree: Differential NMF module expression testing along tree

In farrellja/URD: URD

Description

Differential NMF module expression testing along tree

Usage

moduleTestAlongTree(
  object,
  tips,
  data,
  genelist,
  pseudotime,
  exclude.upstream = F,
  effect.size = log(2),
  p.thresh = 0.01,
  min.expression = 0.1,
  root = NULL,
  must.beat.all.sibs = T
)

Arguments

object	An URD object
tips	(Character) Tip of lineage to do differential expression for
data	(data.frame or matrix) Module expression by cell: rows are modules, columns are cells.
genelist	(List) ?
pseudotime	(Character) Pseudotime to use (i.e. a column name of @pseudotime)
exclude.upstream	(Logical)
effect.size	(Numeric)
p.thresh	(Numeric)
min.expression	(Numeric)
root	(Character)
must.beat.all.sibs	(Logical)

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.