find_top_features {ChromSCape} | R Documentation |
Find the top most covered features that will be used for dimensionality reduction. Optionally remove non-top features.
find_top_features( scExp, n = 20000, keep_others = FALSE, prioritize_genes = FALSE, max_distanceToTSS = 10000, verbose = TRUE )
scExp |
A SingleCellExperiment. |
n |
Either an integer indicating the number of top covered regions to find or a character vector of the top percentile of features to keep (e.g. 'q20' to keep top 20% features). |
keep_others |
Logical indicating if non-top regions are to be removed from the SCE or not (FALSE). |
prioritize_genes |
First filter by loci being close to genes ? E.g. for differential analysis, it is more relevant to keep features close to genes |
max_distanceToTSS |
If prioritize_genes is TRUE, the maximum distance to consider a feature close to a gene. |
verbose |
Print ? |
A SCE with top features
data(scExp) scExp_top = find_top_features(scExp, n = 4000, keep_others = FALSE)