markersBinom: Test for differential gene expression in two populations...

In farrellja/URD: URD

Description

Test for differential gene expression in two populations using a binomial test

Usage

markersBinom(
  object,
  pseudotime,
  clust.1 = NULL,
  clust.2 = NULL,
  cells.1 = NULL,
  cells.2 = NULL,
  clustering = NULL,
  effect.size = log(2),
  p.thresh = 0.01,
  frac.must.express = 0.1,
  genes.use = NULL
)

Arguments

object	An URD object
pseudotime	(Character)
clust.1	(Character)
clust.2	(Character)
cells.1	(Character vector)
cells.2	(Character vector)
clustering	(Character) Name of a clustering (i.e. a column in @group.ids)
effect.size	(Numeric) Minimum log fold-change for two genes to be considered differentially expressed
p.thresh	(Numeric) Minimum significance value for teo genes to be considered expressed
frac.must.express	(Numeric) Gene must be expressed in at least this fraction of cells in one of the two clusters to be considered.
genes.use	(Character vector) Genes to compare, default is NULL (all genes)

Value

(data.frame)

References

Shekhar et al., 2016, Cell 166, 1308–1323

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