get_feature_seqs: Get transcripts features and feature sequences

In SeedMatchR: Find Matches to Canonical SiRNA Seeds in Genomic Features

Get transcripts features and feature sequences

Description

This function is used to get the genomic features of interest and the DNA sequences associated with them. This function takes advantage of the GenomicFeatures package functions threeUTRsByTranscript, fiveUTRsByTranscript, exonsBy, intronsByTranscript, and cdsBy. These functions are used to generate the features given an input tx.db object. A 2bit dna input is also required for extracting features sequences.

The output of the this function is:

• ⁠$db⁠: the feature GRanges object

• ⁠$seqs⁠: DNAStringSet of sequences associated to those features

Usage

get_feature_seqs(tx.db, dna, feature.type = "3UTR")

Arguments

tx.db	A tx.db object
dna	A 2bit dna sequence
feature.type	The type of feature to return. Options: 3UTR, 5UTR, exons, introns, cds

Value

list containing the feature db object and the feature sequences

Examples

anno.db = load_species_anno_db("human")

features = get_feature_seqs(anno.db$tx.db, anno.db$dna)

SeedMatchR documentation built on Oct. 25, 2023, 1:08 a.m.