subset_annot: Subset genome annotation

In lambdamoses/BUStoolsR: kallisto | bustools R utilities

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)

lambdamoses/BUStoolsR documentation built on Aug. 1, 2024, 6:30 a.m.