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
)

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

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

# S4 method for 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

Value

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

A consistent object (to the input) with filled abundance

Details

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

Examples


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