pivot_sample-methods: Extract sample-wise information

In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

Extract sample-wise information

Description

pivot_sample() 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 sample-related columns

Usage

pivot_sample(.data, .sample = NULL)

## S4 method for signature 'spec_tbl_df'
pivot_sample(.data, .sample = NULL)

## S4 method for signature 'tbl_df'
pivot_sample(.data, .sample = NULL)

## S4 method for signature 'tidybulk'
pivot_sample(.data, .sample = NULL)

## S4 method for signature 'SummarizedExperiment'
pivot_sample(.data, .sample = NULL)

## S4 method for signature 'RangedSummarizedExperiment'
pivot_sample(.data, .sample = 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

Details

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

This functon extracts only sample-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_sample(tidybulk::se_mini )

stemangiola/ttBulk documentation built on Dec. 14, 2024, 6:12 a.m.