filter_ambient_barcode: Get filter to remove ambient RNA barcodes based on the...

In keshav-motwani/scanalysis: Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

Description

inflection - all barcodes below the inflection point in the UMI rank vs total UMI plot are called ambient knee - all barcodes below the knee in the UMI rank vs total UMI plot are called ambient cellranger (v2) - all barcodes below 10 empty_drops - uses the algorithm from DropletUtils::emptyDrops to compare each barcode to the profile of barcodes below

Usage

filter_ambient_barcode(
  sce,
  n_cells,
  fdr = 0.01,
  lower_umi_limit = 100,
  n_iters = 10000
)

Arguments

sce	SingleCellExperiment object
n_cells	number of input cells (used in cellranger cutoff computation)
fdr	FDR threshold for keeping a cell for emptyDrops
lower_umi_limit	number of total UMIs below which a barcode is assumed to contain ambient RNA, used in emptyDrops method only

Value

List for each method in containing filter for method and attributes with details specific to each method.

Examples

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keshav-motwani/scanalysis documentation built on Feb. 4, 2021, 2:21 a.m.