impute_missing_abundance-methods: impute transcript abundance if missing from sample-transcript...

In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

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,
  suffix = "",
  force_scaling = FALSE
)

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

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

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

## S4 method for signature 'SummarizedExperiment'
impute_missing_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  suffix = "",
  force_scaling = FALSE
)

## S4 method for signature 'RangedSummarizedExperiment'
impute_missing_abundance(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  suffix = "",
  force_scaling = FALSE
)

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
suffix	A character string. This is added to the imputed count column names. If empty the count column are overwritten
force_scaling	A boolean. In case a abundance-containing column is not scaled (columns with _scale suffix), setting force_scaling = TRUE will result in a scaling by library size, to compensating for a possible difference in sequencing depth.

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
)

stemangiola/ttBulk documentation built on April 10, 2024, 3:36 p.m.