impute_missing_abundance {tidybulk}R Documentation

impute transcript abundance if missing from sample-transcript pairs

Description

impute_missing_abundance() 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 sample-transcript pairs with imputed transcript abundance.

Usage

impute_missing_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL
)

## S4 method for signature 'spec_tbl_df'
impute_missing_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL
)

## S4 method for signature 'tbl_df'
impute_missing_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL
)

## S4 method for signature 'tidybulk'
impute_missing_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL
)

## S4 method for signature 'SummarizedExperiment'
impute_missing_abundance(.data, .formula)

## S4 method for signature 'RangedSummarizedExperiment'
impute_missing_abundance(.data, .formula)

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))

.formula

A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_interest + batch)

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

Details

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

This function imputes the abundance of missing sample-transcript pair using the median of the sample group defined by the formula

Value

A consistent object (to the input) non-sparse abundance

A consistent object (to the input) with imputed abundance

A consistent object (to the input) with imputed abundance

A consistent object (to the input) with imputed abundance

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples



res =
	impute_missing_abundance(
		tidybulk::se_mini,
	~ condition
)



[Package tidybulk version 1.6.1 Index]