filterContaminatedCells: Detecting and removing potentially contaminated cells

In minzheguo/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

Detecting contaminated cells based on the co-expression of highly selectively markers of two different cell types, such as epithelial and endothelial

Usage

filterContaminatedCells(object, do.rm = T, markers.1, markers.2,
  min.expression.1 = 1, min.quantile.1 = 0.99, min.expression.2 = 1,
  min.quantile.2 = 0.99, ...)

Arguments

object	A sincera object
do.rm	If TRUE, remove detected contaminants
markers.1	The vector encoding the markers for one cell type
markers.2	The vector encoding the markers for the other cell type
min.expression.1	The threshold value of the expression of markers in markers.1
min.quantile.1	The threshold value of the expression quantile of markers in markers.1
min.expression.2	The threshold value of the expression of markers in markers.2
min.quantile.2	The threshold value of the expression quantile of markers in markers.2

Value

An updated sincera object with detected contaminated cells removed

minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.