filterGenesSample: filterGenesSample

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description

Given a set of genes, filter to the ones found in the sample. This is useful because some Seurat functions (Seurat::VlnPlot, Seurat::FeaturePlot) will quit on an error if a gene is not found (i.e. not in the rownames of seurat@data).

Usage

filterGenesSample(genes, seurat, from_sp = "hg", to_sp = "mm")

Arguments

genes	Character vector of genes to search for
seurat	Seurat object
from_sp	One of "hg" or "mm". Default: "hg"
to_sp	One of "hg" or "mm". Default: "mm"

Value

Character vector of converted gene names which are detected in the sample

Author(s)

adapted from Claudia Kleinman

Examples

filterGenesSample(c("IL32", "foo"), pbmc, "hg", "hg")

fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.