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

In stemangiola/tidyBulk: Brings transcriptomics to the tidyverse

Fill transcript abundance if missing from sample-transcript pairs

Description

fill_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 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
)

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

questioning

This function fills 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 filled abundance

A consistent object (to the input) with filled abundance

A consistent object (to the input) with filled abundance

Examples

print("Not run for build time.")

# tidybulk::se_mini |>  fill_missing_abundance( fill_with = 0)

stemangiola/tidyBulk documentation built on Oct. 22, 2024, 5:19 a.m.