pivot_transcript-methods: Extract transcript-wise information

In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

Extract transcript-wise information

Description

pivot_transcript() 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 'tbl' with only transcript-related columns

Usage

pivot_transcript(.data, .transcript = NULL)

## S4 method for signature 'spec_tbl_df'
pivot_transcript(.data, .transcript = NULL)

## S4 method for signature 'tbl_df'
pivot_transcript(.data, .transcript = NULL)

## S4 method for signature 'tidybulk'
pivot_transcript(.data, .transcript = NULL)

## S4 method for signature 'SummarizedExperiment'
pivot_transcript(.data, .transcript = NULL)

## S4 method for signature 'RangedSummarizedExperiment'
pivot_transcript(.data, .transcript = 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))
.transcript	The name of the transcript column

Details

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

This functon extracts only transcript-related information for downstream analysis (e.g., visualisation). It is disruptive in the sense that it cannot be passed anymore to tidybulk function.

Value

A 'tbl' with transcript-related information

A consistent object (to the input)

A consistent object (to the input)

Examples

	pivot_transcript(tidybulk::se_mini 	)

stemangiola/ttBulk documentation built on Oct. 19, 2024, 1:34 p.m.