impute_abundance {tidybulk}R Documentation

Impute transcript abundance if missing from sample-transcript pairs

Description

impute_abundance() takes as imput a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with an edditional adjusted abundance column. This method uses scaled counts if present.

Usage

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

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

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

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

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

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

Arguments

.data

A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

.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_intrest + 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

Maturing lifecycle

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

Value

A 'tbl' non-sparse abundance

A 'tbl' with imputed abundnce

A 'tbl' with imputed abundnce

A 'tbl' with imputed abundnce

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples



res =
	impute_abundance(
		tidybulk::counts_mini,
	~ condition,
	.sample = sample,
	.transcript = transcript,
	.abundance = count
)



[Package tidybulk version 1.0.2 Index]