dataSubsetBySparsity: Filter scATACseq by sparsity

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

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 Feb. 8, 2023, 6:46 p.m.