ensembl_to_symbol {tidybulk} | R Documentation |
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
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")
.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). |
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.
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
library(dplyr) tidybulk::counts_SE |> tidybulk() |> as_tibble() |> ensembl_to_symbol(feature)