aucprTestAlongTree: Test for differential gene expression along tree using...
In farrellja/URD: URD

Description Usage Arguments Details Value

This test performs differential expression testing along URD's recovered tree structure using the area under a precision-recall curve (see: markersAUCPR) to determine how good individual genes are as markers of a lineage.

aucprTestAlongTree(
  object,
  pseudotime,
  tips,
  log.effect.size = 0.25,
  auc.factor = 1,
  max.auc.threshold = 1,
  frac.must.express = 0.1,
  frac.min.diff = 0.1,
  genes.use = NULL,
  root = NULL,
  segs.to.skip = NULL,
  only.return.global = F,
  must.beat.sibs = 0.5,
  report.debug = F
)

`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 mean expression to be considered differential (default, `log(2)` is 2-fold change)
`auc.factor`	(Numeric) The precision-recall AUC is determined for a random classifier is determined based on the size of populations. To be considered differential, genes must have an AUC this factor multiplied by the expected AUC of a random classifier.
`max.auc.threshold`	(Numeric) This acts as an upper bound for how high the AUC must be for a gene to be considered differential.
`frac.must.express`	(Numeric) Fraction of cells of interest that must express the gene to consider it differential.
`frac.min.diff`	(Numeric) Minimum difference in fraction of cells expressing a 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)
`segs.to.skip`	(Character vector) Are there any segments in the tree that should not be used for testing differential expression? (Default, `NULL` will test all segments.)
`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.debug`	(Logical) If `TRUE`, this function returns a list instead of a data.frame, with `$stats` containing information about all of the comparisons? (nGene, nTrans, pseudotime, n.cells) and `$marker.chain` containing the markers from each branchpoint.

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.

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

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