dataSubsetBySparsity: Filter scATACseq by sparsity

View source: R/dataSubset_by_sparsity.R

dataSubsetBySparsityR Documentation

Filter scATACseq by sparsity

Description

Function to filter a set of scATACseq data by sparsity and return a subset of filtered data, as well as list of the remaining cells and peaks.

Usage

dataSubsetBySparsity(
  data,
  cell_list,
  peak_list,
  cell_cut = 0.99,
  peak_cut = 0.99
)

Arguments

data

matrix of read counts peaks x cells

cell_list

list of cell names/identifiers for the data

peak_list

list of peaks from the data

cell_cut

threshold of sparsity to filter at (eg. 0.99 filters all cells with more than 99 percent zero values)

peak_cut

threshold of sparsity to filter at for peaks

Value

nested list containing the subset data, a list of peaks, and list of cells

Examples

data("subsetSchepData")
data("schepPeaks")
data("schepCellTypes")

outData = dataSubsetBySparsity(subsetSchepData, schepCellTypes, schepPeaks)
  

FertigLab/ATACCoGAPS documentation built on June 29, 2022, 4:13 p.m.