keep_variable {tidybulk}R Documentation

Keep variable transcripts

Description

keep_variable() 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 additional columns for the statistics from the hypothesis test.

Usage

keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  log_transform = TRUE
)

## S4 method for signature 'spec_tbl_df'
keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  log_transform = TRUE
)

## S4 method for signature 'tbl_df'
keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  log_transform = TRUE
)

## S4 method for signature 'tidybulk'
keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  log_transform = TRUE
)

## S4 method for signature 'SummarizedExperiment'
keep_variable(.data, top = 500, log_transform = TRUE)

## S4 method for signature 'RangedSummarizedExperiment'
keep_variable(.data, top = 500, log_transform = TRUE)

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

top

Integer. Number of top transcript to consider

log_transform

A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)

Details

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

At the moment this function uses edgeR https://doi.org/10.1093/bioinformatics/btp616

Value

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

Underlying method: s <- rowMeans((x - rowMeans(x)) ^ 2) o <- order(s, decreasing = TRUE) x <- x[o[1L:top], , drop = FALSE] variable_trancripts = rownames(x)

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples




	keep_variable(
	tidybulk::se_mini,
	    top = 500
	)



[Package tidybulk version 1.6.1 Index]