ssc.build: Build an SingleCellExperiment object

In Japrin/sscVis: simpler single cell RNAseq data Visualization

Build an SingleCellExperiment object

Description

Build an SingleCellExperiment object from a matrix or data frame

Usage

ssc.build(x, display.name = NULL, assay.name = "exprs")

Arguments

x	matrix/data.frame or SingleCellExperiment; input expression data
display.name	a vector, should be human readable gene name
assay.name	assay name (default "exprs")

Details

if x is an object of SingleCellExperiment, just clear the metadata; if x is matrix/data.frame, convert it to an object of SingleCellExperiment. Also a vector 'display.name' can be provided, which would be used in some plots, such as geneOnTSNE, heatmap. The row names of SingleCellExperiment object usually be gene id (e.g. entrez ID, Ensemble ID), the 'display.name' should be human readable gene name ( e.g. HGNC gene symbol). If 'display.name' is NULL (default), the row names of SingleCellExperiment object would be used.

Value

an object of SingleCellExperiment class

Japrin/sscVis documentation built on March 5, 2025, 10:23 a.m.