Skip to contents

Filter features by summary statistics

Source: R/feature_selection.R
filter_features.Rd

Remove ATAC peaks with low coverage, or that are too long etc.

Usage

filter_features(
  atac_sc,
  minimal_max_umi = NULL,
  min_peak_length = NULL,
  max_peak_length = NULL,
  max_peak_density = NULL
)

Arguments

atac_sc

the ScPeaks object to analyze

minimal_max_umi

(optional) threshold on minimum maximal coverage - i.e. remove all peaks that DON'T have a cell with at least abs_cov_thresh UMIs

min_peak_length

(optional) remove all peaks that are less than min_cov_thresh base-pairs long

max_peak_length

(optional) remove all peaks that are more than min_cov_thresh base-pairs long

max_peak_density

(optional) remove all peaks that have more than max_peak_density UMIs per 100bp

Value

atac_sc - the filtered ScPeaks object

Examples

if (FALSE) {
## quantiles of peak lengths before filtering
quantile(my_atac_sc@peaks$end - my_atac_sc@peaks$start, (0:10) / 10)
my_atac_sc <- filter_features(atac_sc = my_atac_sc, minimal_max_umi = 3, min_peak_length = 200, max_peak_length = 1000)

## quantiles of peak lengths after filtering
quantile(my_atac_sc@peaks$end - my_atac_sc@peaks$start, (0:10) / 10)
}