ensembl_to_symbol-methods: Add transcript symbol column from ensembl id for human and...
In stemangiola/tidyBulk: Brings transcriptomics to the tidyverse

ensembl_to_symbol

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

\lifecycle

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

Examples




# This function was designed for data.frame
# Convert from SummarizedExperiment for this example. It is NOT reccomended.

tidybulk::se_mini |> tidybulk() |> as_tibble() |> ensembl_to_symbol(.feature)

stemangiola/tidyBulk documentation built on April 13, 2024, 8:13 a.m.