getAnnotation: getAnnotation

In swaruplabUCI/ArchRtoSignac: What the Package Does (One Line, Title Case)

getAnnotation

Description

This function gets the gene annotation, which includes information related to genomic locations and their associated annotations, from Ensembl Database in GRanges Object for the Seurat object. Then it changes the annotation to the UCSC style (default).

Usage

getAnnotation(reference, seqStyle = "UCSC", refversion)

Arguments

reference	An Ensembl genome reference used for the Signac function GetGRangesFromEnsDb to extract gene annotations from EnsDb (for example: EnsDb.Hsapiens.v86)
seqStyle	Sequence style to change the annotation extracted from EnsDb to (default is ‘UCSC’)
refversion	The assembly release and versions of UCSC genome reference (for example: 'hg38')

Examples

annotations <- getAnnotation(reference = EnsDb.Hsapiens.v86, seqStyle = 'UCSC', refversion = 'hg38')

swaruplabUCI/ArchRtoSignac documentation built on Aug. 23, 2024, 2:03 p.m.