find_top_features {ChromSCape} | R Documentation

## 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)

[Package ChromSCape version 1.2.62 Index]