feature_annotation_scExp: Add gene annotations to features

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

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' or 'mm10'. ('hg38')
reference_annotation	A data.frame containing gene (or else) annotation with genomic coordinates.

Value

A SingleCellExperiment object with annotated rowData.

Examples

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

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

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.