binomTestAlongTree: Test for differential gene expression along tree using...

In farrellja/URD: URD

Description

This test performs differential expression testing along URD's recovered tree structure using a binomial expression test (see: markersBinom).

Usage

binomTestAlongTree(
  object,
  pseudotime,
  tips,
  log.effect.size = log(2),
  p.thresh = 0.01,
  frac.must.express = 0.1,
  genes.use = NULL,
  root = NULL,
  only.return.global = F,
  must.beat.sibs = 0.5,
  report.stats = F
)

Arguments

object	An URD object
pseudotime	(Character) Name of pseudotime to use
tips	(Character vector) The tip of the trajectory to find differential expression for (either as tip number or name)
log.effect.size	(Numeric) Minimum fold-change difference in expression to be considered differential (default, log(2) is 2-fold change)
p.thresh	(Numeric) Significance threshold for being considered differential
frac.must.express	(Numeric) Fraction of cells of interest that must express the gene to consider it differential.
genes.use	(Character vector) Which genes to test for differential expression (default NULL is all genes)
root	(Character) Which segment of the tree (by number) to use as the root for differential express (default NULL will autodetect, but this can be useful if you do not want to traverse up the entire tree)
only.return.global	(Logical) Genes must also pass an overall in-trajectory vs. out-of-trajectory test across all cells in the data to be considered differential (default, FALSE)
must.beat.sibs	(Numeric) At multi-furcated branchpoints, independent comparisons are made to each sibling. For a gene to be considered differential it must be a marker against this proportion of its sibling branches. (1 means it must be a marker against all other branches, 0 means it must be a marker against a single other branch.)
report.stats	(Logical) Should information be returned about all of the comparisons? (nGene, nTrans, pseudotime, n.cells) If TRUE, this function returns a list instead of a data.frame

Details

It starts from the segment provided in tips and compares it to each of its siblings (and their descendants) matched to the same pseudotime limits as the segment under consideration. Markers that are upregulated in a segment compared to either any of its siblings (if must.beat.all.sibs=FALSE) or compared to each of its siblings (if must.beat.all.sibs=TRUE) become putative markers.

Value

a data.frame of gene expression results if report.stats=F or a list with entries diff.exp and stats if report.stats=T.

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