getSequenceFeatures: Get sequence features from orfik

In Roleren/uORFomePipe: uORF prediction in R

Get sequence features from orfik

Description

Get sequence features from orfik

Usage

getSequenceFeatures(
  organism,
  biomart,
  grl = uORFomePipe:::getUorfsInDb(),
  mode = "uORF"
)

Arguments

organism	scientific name of organism, like Homo sapiens, Danio rerio, etc.
biomart	default "ensembl", get gene symbols and GO terms for uORF genes. Will be automaticly detected by organism name in ensembl database. Set to NULL if you don't want to check Gene symbols and GO terms.
grl	the orfs as GRangesList, default uORFomePipe:::getUorfsInDb()
mode	character, default: "uORF". alternative "aCDS". Do you want to predict on uORFs or artificial CDS. if "aCDS" will run twice once for whole length CDS and one for truncated CDS to validate model works for short ORFs. "CDS" is option to predict on whole CDS.

Value

return(invisible(NULL)

Roleren/uORFomePipe documentation built on Jan. 14, 2024, 5:11 a.m.