ensembl_to_symbol {tidybulk}R Documentation

Add transcript symbol column from ensembl id for human and mouse data

Description

ensembl_to_symbol() takes as input a 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and returns a consistent object (to the input) with the additional transcript symbol column

Usage

ensembl_to_symbol(.data, .ensembl, action = "add")

## S4 method for signature 'spec_tbl_df'
ensembl_to_symbol(.data, .ensembl, action = "add")

## S4 method for signature 'tbl_df'
ensembl_to_symbol(.data, .ensembl, action = "add")

## S4 method for signature 'tidybulk'
ensembl_to_symbol(.data, .ensembl, action = "add")

Arguments

.data

a 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))

.ensembl

A character string. The column that is represents ensembl gene id

action

A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).

Details

[Questioning]

This is useful since different resources use ensembl IDs while others use gene symbol IDs. At the moment this work for human (genes and transcripts) and mouse (genes) data.

Value

A consistent object (to the input) including additional columns for transcript symbol

A consistent object (to the input) including additional columns for transcript symbol

A consistent object (to the input) including additional columns for transcript symbol

A consistent object (to the input) including additional columns for transcript symbol

Examples


library(dplyr)

tidybulk::counts_SE |> tidybulk() |> as_tibble() |> ensembl_to_symbol(feature)




[Package tidybulk version 1.6.1 Index]