get_annotations: This function annotates a column of transcripts or gene IDs...

In davidrequena/drfun: Functions To Help With RNAseq Data Analysis

This function annotates a column of transcripts or gene IDs (ENSEMBL) with information of the Biomart. If transcript IDs are provided, they are also annotated with information of the genes to which they belong.

Description

The Gene information added include:

• Gene ENSEMBL ID, HGNC Symbol, Description, Biotype and Chromosome.

• Gene start, end and length

Usage

get_annotations(
  ensembl_ids,
  mode = "genes",
  filename = "gene_annotations",
  version = "",
  format = "csv"
)

Arguments

ensembl_ids	The column of transcripts to be used as input.
mode	To specify the IDs provided, between "transcripts" or "genes". Default = genes.
filename	The name of the output file, which is table. Default = gene_annotations.
version	This function can use the version 103 or the current version of the Biomart. Default = Current.
format	The output is saved in .csv or .xlsx formats. Default = csv.

davidrequena/drfun documentation built on May 15, 2024, 10:33 a.m.