Decontaminate: Main function

Description Usage Arguments Value

View source: R/veni.R

Description

Main function

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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.