Description Usage Arguments Details Value
This test performs differential expression testing along URD's recovered tree
structure using a binomial expression test (see: markersBinom
).
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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
)
|
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, |
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 |
root |
(Character) Which segment of the tree (by number) to use as the root for differential express (default |
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, |
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 |
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.stats=F
or a list with entries diff.exp
and stats
if report.stats=T
.
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