Decontaminate: Main function

In mathewchamberlain/veni: Generates QC plots, performs ambient RNA removal, and enhanced differential from single cell RNA sequencing data

Description

Main function

Usage

Decontaminate(
  E,
  B,
  min_genes_before = 0,
  min_genes_after = 0,
  min_umi_before = 0,
  min_umi_after = 0,
  do.par = FALSE,
  num.cores = NULL,
  large = FALSE,
  num.chunks = 20
)

Arguments

E	Expression matrix or a list of expression matrices
B	Background matrix or a list of background matrices (see ?GetBackground)
min_genes_before	All barcodes with less than min_genes_before detected will be removed prior to background correction.
min_genes_after	All barcodes with less than min_genes_after detected will be removed after background correction.
min_umi_before	All barcodes with less than min_umi_before will be removed prior to background correction.
min_umi_after	All barcodes with less than min_umi_after will be removed after background correction.
do.par	If TRUE, regressions will be done in parallel
num.cores	Set number of cores for parallel computation. By default, all available cores - 1 will be used.
large	if TRUE, dataset is chunked prior to regression to prevent any memory errors.
num.chunks	if large, the dataset is chunked into num.chunks, and then regressed in parallel.

Value

Background corrected expression matrices

mathewchamberlain/veni documentation built on Oct. 9, 2020, 2:30 a.m.