Fill transcript abundance if missing from sample-transcript pairs

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

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

Value

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

Details

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

References

Mangiola, S., Molania, R., Dong, R., Doyle, M. A., & Papenfuss, A. T. (2021). tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biology, 22(1), 42. doi:10.1186/s13059-020-02233-7

Examples

## Load airway dataset for examples

  data('airway', package = 'airway')
  # Ensure a 'condition' column exists for examples expecting it

    SummarizedExperiment::colData(airway)$condition <- SummarizedExperiment::colData(airway)$dex



print("Not run for build time.")
#> [1] "Not run for build time."

# airway |>  fill_missing_abundance( fill_with = 0)