fill_missing_abundance-methods: Fill transcript abundance if missing from sample-transcript...

In tidybulk: Brings transcriptomics to the tidyverse

Description

fill_missing_abundance() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with new observations

Usage

fill_missing_abundance(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  fill_with
)

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

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

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

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

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

Arguments

.data	A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.sample	The name of the sample column
.transcript	The name of the transcript column
.abundance	The name of the transcript abundance column
fill_with	A numerical abundance with which fill the missing data points

Details

\lifecycle

maturing

This function fills 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 filled abundance

A 'tbl' with filled abundance

A 'tbl' with filled abundance

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

fill_missing_abundance(tidybulk::counts_mini, sample, transcript, count, fill_with = 0)

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