get_gene_names: Get Gene Names from an Expression Matrix or a Seurat object

In chenyenchung/genofeatutil: Utilities for genomic feature manipulation

Description

get_gene_names() extracts gene names from a matrix, data frame, or Seurat object. For a martix or data frame, you need to tell it whether the gene names are in row names or column names. If it's a Seurat object, you'll need to specify the assay you want.

Usage

get_gene_names(x, ...)

## Default S3 method:
get_gene_names(x, use.row = FALSE, ...)

## S3 method for class 'Seurat'
get_gene_names(x, assay = "RNA", ...)

Arguments

x	an object (matrix, data frame, or Seuratv3 object) to extract gene names from
...	other arguments passing to S3 methods (see below)
use.row	a logical constant indicating whether the gene names are in row names or not
assay	a character string indicating an assay in the Seurat object

Value

a character vector

Examples

# Create a dummy expression matrix
expression_df <- data.frame(
"sample1" = c(1:10),
"sample2" = c(1:10),
"sample3" = c(1:10)
)

row.names(expression_df) <- c(paste("gene", c(1:10), sep = ""))

# Create Seurat object from the dummy data
seuratobj <- Seurat::CreateSeuratObject(counts = expression_df,
                                        assay = "RNA")
# Get gene names from a data frame
get_gene_names(expression_df, use.row = TRUE)

# Get gene names from a Seuratv3 object
get_gene_names(seuratobj, assay = "RNA")

chenyenchung/genofeatutil documentation built on May 15, 2019, 10:38 p.m.