tidybulk-methods: Creates an annotated 'tidybulk' tibble from a 'tbl' or...
In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

tidybulk

R Documentation

Creates an annotated 'tidybulk' tibble from a 'tbl' or 'SummarizedExperiment' object

Description

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

Usage

tidybulk(.data, .sample, .transcript, .abundance, .abundance_scaled = NULL)

## S4 method for signature 'spec_tbl_df'
tidybulk(.data, .sample, .transcript, .abundance, .abundance_scaled = NULL)

## S4 method for signature 'tbl_df'
tidybulk(.data, .sample, .transcript, .abundance, .abundance_scaled = NULL)

## S4 method for signature 'SummarizedExperiment'
tidybulk(.data, .sample, .transcript, .abundance, .abundance_scaled = NULL)

## S4 method for signature 'RangedSummarizedExperiment'
tidybulk(.data, .sample, .transcript, .abundance, .abundance_scaled = NULL)

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))
`.sample`	The name of the sample column
`.transcript`	The name of the transcript/gene column
`.abundance`	The name of the transcript/gene abundance column
`.abundance_scaled`	The name of the transcript/gene scaled abundance column

Details

'r lifecycle::badge("maturing")'

This function creates a tidybulk object and is useful if you want to avoid to specify .sample, .transcript and .abundance arguments all the times. The tidybulk object have an attribute called internals where these three arguments are stored as metadata. They can be extracted as attr(<object>, "internals").