feature_annotation_scExp: Add gene annotations to features

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Add gene annotations to features

Description

Add gene annotations to features

Usage

feature_annotation_scExp(scExp, ref = "hg38", reference_annotation = NULL)

Arguments

scExp	A SingleCellExperiment object.
ref	Reference genome. Either 'hg38', 'mm10' or 'ce11'. ('hg38')
reference_annotation	A data.frame containing gene (or else) annotation with genomic coordinates.

Value

A SingleCellExperiment object with annotated rowData.

Examples

raw <- create_scDataset_raw()
scExp = create_scExp(raw$mat, raw$annot)
scExp = feature_annotation_scExp(scExp)
head(SummarizedExperiment::rowRanges(scExp))

# Mouse
raw = create_scDataset_raw(ref = "mm10")
scExp = create_scExp(raw$mat, raw$annot)
scExp = feature_annotation_scExp(scExp,ref="mm10")
head(SummarizedExperiment::rowRanges(scExp))

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.