keep_variable-methods: Keep variable transcripts

keep_variableR 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,
  transform = log1p,
  log_transform = TRUE
)

## S4 method for signature 'spec_tbl_df'
keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  transform = log1p,
  log_transform = NULL
)

## S4 method for signature 'tbl_df'
keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  transform = log1p,
  log_transform = NULL
)

## S4 method for signature 'tidybulk'
keep_variable(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  transform = log1p,
  log_transform = NULL
)

## S4 method for signature 'SummarizedExperiment'
keep_variable(.data, top = 500, transform = log1p)

## S4 method for signature 'RangedSummarizedExperiment'
keep_variable(.data, top = 500, transform = log1p)

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

transform

A function that will tranform the counts, by default it is log1p for RNA sequencing data, but for avoinding tranformation you can use identity

log_transform

DEPRECATED - 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)



stemangiola/tidyBulk documentation built on Nov. 21, 2024, 8:14 a.m.