which_genes_regex: Get indices of genes whose annotation matches a regex.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Get indices of genes whose annotation matches a regex.

Description

Get indices of genes whose annotation matches a regex.

Usage

which_genes_regex(sce, regex, colname = "Symbol", ignore_case = TRUE)

Arguments

sce	A SingleCellExperiment object.
regex	A character scalar.
colname	A character scalar: name of column in rowData(sce) whose values will be tested by regex.
ignore_case	A logical scalar: if TRUE, ignore case in regex.

Value

An integer vector: indices of rowData(sce) matching the regex.

Examples

## Not run: 
# Indices of mitochondrial genes.
which_genes_regex(sce, regex = "^MT-", colname = "Symbol", ignore_case = TRUE)

## End(Not run)

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.