subset_annot {BUSpaRse} | R Documentation

## Subset genome annotation

### Description

Exclude chromosomes present in the annotation but absent from the genome and add information about circular chromosomes.

### Usage

    subset_annot(Genome, annot)

    ## S4 method for signature 'DNAStringSet'
    subset_annot(Genome, annot)

    ## S4 method for signature 'BSgenome'
    subset_annot(Genome, annot)

### Arguments

`Genome` | Either a `BSgenome` or a `XStringSet` object of genomic sequences, where the intronic sequences will be extracted from. Use `genomeStyles` to check which styles are supported for your organism of interest; supported styles can be interconverted. If the style in your genome or annotation is not supported, then the style of chromosome names in the genome and annotation should be manually set to be consistent.
`annot` | Either a `GRanges` object or a `TxDb` object for gene annotation.

### Value

A subsetted genome annotation of the same type of the input genome annotation.

### Examples

    library(BSgenome.Hsapiens.UCSC.hg38)
    library(EnsDb.Hsapiens.v86)
    library(GenomeInfoDb)
    gn <- BSgenome.Hsapiens.UCSC.hg38
    seqlevelsStyle(gn) <- "Ensembl"
    subset_annot(gn, EnsDb.Hsapiens.v86)

[Package BUSpaRse version 1.4.2 Index]