Snitch: Get sequence

In fursham-h/quafle: Quantifying Usage of Alternative First and Last Exons

Get sequence

Description

Get sequence

Usage

Snitch(
  se,
  fasta,
  subset = NULL,
  type = c("start", "end", "exon"),
  exontype = c("all", "AF", "AL"),
  upstream = 50,
  downstream = 50,
  outdir = NULL,
  filename = "Snitch.fasta"
)

Arguments

se	RangedSummarizedExperiment object from 'Quaffle' output
fasta	BSGenome object or DNAStringList object containing genome sequence
subset	A character vector containing IDs to subset. IDs can be name of genes, ID of genes or AFL coordinates
type	Type of sequence to return. Can be the start of exon ("start"), end of exon ("end") or entire exon ("exon")
exontype	Type of event to return, Can be "all", "AF" or "AL"
upstream	Length of upstream padding sequence
downstream	Length of downstream padding sequence
outdir	Path to output directory (Default: only return DNAStringSet object)
filename	Name of FASTA file to create

Value

DNAStringSet object with DNA sequences of selected events

fursham-h/quafle documentation built on Oct. 9, 2022, 4:49 p.m.