keep_variable-methods: Keep variable transcripts

In tidybulk: Brings transcriptomics to the tidyverse

Description

keep_variable() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' 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,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  top = 500,
  log_transform = TRUE
)

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

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
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

\lifecycle

maturing

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

Value

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

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

A 'tbl' 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::counts_mini,
	    sample,
	    transcript,
	    `count`,
	    top = 500
	)

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