fitDynamic {CellTrails} | R Documentation |
Fits feature expression as a function of pseudotime along a defined trail.
fitDynamic(sce, feature_name, trail_name)
sce |
A |
feature_name |
Name of feature |
trail_name |
Name of trail |
A trail is an induced subgraph of the trajectory graph. A
trajectory graph is composed of samples (nodes) that are connected
(by weighted edges) if they are chronologically related. A trail has to be
defined by the user using addTrail
. A pseudotime vector is extracted
by computing the geodesic distance for each sample from the trail's start
node. To infer the expression level of a feature as a function of
pseudotime, CellTrails used generalized additive models with a single
smoothing term with four basis dimensions. Here, for each feature CellTrails
introduces prior weights for each observation to lower the confounding
effect of drop-outs to the maximum-likelihood-based fitting process as
follows. Each non-detect of feature
j in state h is weighted by the relative fraction of
non-detects of feature j in state h; detected values are
always assigned weight = 1.
An object of type list
with the following components
pseudotime
The pseudotime along the trail
expression
The fitted expression values for each value of pseudotime
gam
A object of class gamObject
Daniel C. Ellwanger
addTrail
gamObject
# Example data data(exSCE) # Fit dynamic fit <- fitDynamic(exSCE, feature_name="feature_3", trail_name="Tr1") summary(fit)