getBiomarker: Given a list of genes and a SingleCellExperiment object,...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Given a list of genes and a SingleCellExperiment object, return the binary or continuous expression of the genes.

Description

Given a list of genes and a SingleCellExperiment object, return the binary or continuous expression of the genes.

Usage

getBiomarker(
  inSCE,
  gene,
  binary = "Binary",
  useAssay = "counts",
  featureLocation = NULL,
  featureDisplay = NULL
)

Arguments

inSCE	Input SingleCellExperiment object.
gene	gene list
binary	"Binary" for binary expression or "Continuous" for a gradient. Default: "Binary"
useAssay	Indicates which assay to use. The default is "counts".
featureLocation	Indicates which column name of rowData to query gene.
featureDisplay	Indicates which column name of rowData to use to display feature for visualization.

Value

getBiomarker(): A data.frame of expression values

Examples

data("mouseBrainSubsetSCE")
getBiomarker(mouseBrainSubsetSCE, gene="C1qa")

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.