filterTrajFeaturesByDL {CellTrails} | R Documentation |
Filters trajectory features that are detected in a minimum number of samples.
filterTrajFeaturesByDL(sce, threshold, show_plot = TRUE)
sce |
An |
threshold |
Minimum number of samples; if value < 1 it is interpreted as fraction, otherwise as absolute sample count |
show_plot |
Indicates if plot should be shown (default: TRUE) |
The detection level denotes the fraction of samples in which a
feature was detected. For each trajectory feature listed in the
CellTrailsSet object the relative number of samples having a feature
expression value greater than 0 is counted. Features that are expressed in
a fraction of all samples greater than threshold
remain labeled as
trajectory feature as listed in the SingleCellExperiment
object,
otherwise they may be not considered for dimensionality reduction,
clustering, and trajectory reconstruction. If the parameter threshold
fullfills threshold
>= 1 it becomes converted to a relative
fraction of the total sample count. Please note that spike-in controls
are ignored and are not listed as trajectory features.
A character
vector
Daniel C. Ellwanger
trajFeatureNames
isSpike
# Example data set.seed(1101) dat <- simulate_exprs(n_features=15000, n_samples=100) # Create container alist <- list(logcounts=dat) sce <- SingleCellExperiment(assays=alist) # Filter features tfeat <- filterTrajFeaturesByDL(sce, threshold=2) head(tfeat) # Set trajectory features to object trajFeatureNames(sce) <- tfeat # Number of features length(trajFeatureNames(sce)) #filtered nrow(sce) #total