PerformEmptyDropletFiltering: PerformEmptyDropletFiltering

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

PerformEmptyDropletFiltering

Description

PerformEmptyDropletFiltering

Usage

PerformEmptyDropletFiltering(
  seuratRawData,
  fdrThreshold = 0.001,
  emptyDropNIters = 10000,
  emptyDropsLower = 200,
  useEmptyDropsCellRanger = FALSE,
  nExpectedCells = 8000
)

Arguments

seuratRawData	Raw data
fdrThreshold	FDR threshold, passed directly to PerformEmptyDrops()
emptyDropNIters	Number of iterations, passed directly to PerformEmptyDrops()
emptyDropsLower	Passed directly to emptyDrops(). The lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets.
useEmptyDropsCellRanger	If TRUE, will use DropletUtils emptyDropsCellRanger instead of emptyDrops
nExpectedCells	Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument

Value

Plot

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.