getExpr: Get gene expression matrix from input data object

In BaderLab/Tempora: Pathway-based Trajectory Inference for Time-series Single Cell RNA-Seq Data

Description

Extract the gene expression matrix from a single-cell data object containing the input data for scClustViz visualization.

Usage

getExpr(x, assayType, assaySlot)

Arguments

x	The single-cell data object.
assayType	A length-one character vector representing the assay object in which the expression data is stored in the input object. For Seurat v1 or v2 objects, set this to "". For Seurat v3 objects, this is often "RNA". For SingleCellExperiment objects, this is often "logcounts". See Details for how this argument is used in the accessor functions for each class.
assaySlot	An optional length-one character vector representing the slot of the Seurat v3 Assay object to use. In Seurat v3, normalized data is stored in the "data" slot, and counts in the "counts" slot. See Details for how this argument is used in the accessor functions for each class.

Details

This is a wrapper function to the relevant class's normalized data slot accessor method. Currently supported input object classes:

• Class seurat/Seurat stored in x@data or x@assays[[assayType]]@assaySlot, depending on Seurat object version.

• Class SingleCellExperiment accessed by assay(x,assayType).

Please submit requests for other data objects here!

Author(s)

Contributed by Brendan Innes from the BaderLab/scClustViz package

BaderLab/Tempora documentation built on April 25, 2021, 2:10 p.m.