filter_segments: Filter segments.

In Militeee/rcongas: Copy Number Alterations genotyping from single-cell multiomics

Filter segments.

Description

After mapping data to segments, this function can be used to remove segments that are too short, or that have too few mapped RNA genes or ATAC peaks. A parameters allows to input a list of segments that will be retained no matter what.

The function requires and returns an (R)CONGAS+ object.

Usage

filter_segments(
  x,
  length = 0,
  RNA_genes = 50,
  ATAC_peaks = 50,
  segments = list(),
  RNA_nonzerocells = 0,
  ATAC_nonzerocells = 0
)

Arguments

x	An rcongasplus object.
length	Mimium size in number of bases for each segment. This is 0 by default, and therefore non effective.
RNA_genes	Required number of RNA genes, if RNA is available. This is 50 by default.
ATAC_peaks	Required number of ATAC peaks, if ATAC is available. This is 50 by default.
segments	A list of segment ids to retain regardless of the filters.

Value

The object x where segments have been identified and removed.

Examples

data('example_object')

# Default
print(example_object)

example_object %>% 
  filter_segments() %>% 
  print()

# Minimum size
example_object %>% 
  filter_segments(length = 1e7) %>% 
  print()

Militeee/rcongas documentation built on Nov. 1, 2024, 2:38 a.m.