find_top_features: Find most covered features

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Find most covered features

Description

Find the top most covered features that will be used for dimensionality reduction. Optionally remove non-top features.

Usage

find_top_features(
  scExp,
  n = 20000,
  keep_others = FALSE,
  prioritize_genes = FALSE,
  max_distanceToTSS = 10000,
  verbose = TRUE
)

Arguments

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 ?

Value

A SCE with top features

Examples

data(scExp)
scExp_top = find_top_features(scExp, n = 4000, keep_others = FALSE)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.