tidybulk-methods: Creates a 'tt' object from a 'tbl' or 'SummarizedExperiment'...

In tidybulk: Brings transcriptomics to the tidyverse

Description

tidybulk() creates a 'tt' object from a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

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' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.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

\lifecycle

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").

Value

A 'tidybulk' object

A 'tidybulk' object

A 'tidybulk' object

A 'tidybulk' object

A 'tidybulk' object

Examples

my_tt =  tidybulk(tidybulk::counts_mini, sample, transcript, count)

tidybulk documentation built on April 7, 2021, 6 p.m.