Apply documented corrections to a manifest

Applies a corrections table to a long-format manifest, one row per sample, and records what changed. A study keeps its overrides in one table with a reason for each, instead of inline edits spread over scripts.

Usage

apply_corrections(manifest, corrections)

Arguments

manifest

A data frame with one row per sample and at least a subject_id and a sample_id column.

corrections

A data frame with columns level, id, column, value, and reason. level is "subject" or "sample". id names the subject or sample. column names the manifest column to change and value is the new value. See read_corrections() to read one from a file.

Value

The corrected manifest as a tibble. The "corrections" attribute holds the audit table, which corrections_log() returns.

Details

A subject correction changes every manifest row for that subject. A sample correction changes the row or rows for that sample. Corrections are applied in order, so a later row can overwrite an earlier one for the same cell. A corrected column becomes character, and an NA value clears the cell.

The audit table has one row per correction: level, id, column, old_value, new_value, reason, and n_rows, the number of manifest rows that changed. When the old values differ across those rows they are joined with "; ". Applying corrections to an already corrected manifest appends to the existing audit table.

The function errors when a required column of corrections is missing, when a level is not "subject" or "sample", when an id is not in the manifest, or when a column is not in the manifest.

See also

read_corrections(), corrections_log()

Examples

manifest <- tibble::tibble(
  subject_id = c("R1", "R1", "R2"),
  assay = c("wes", "wes", "wes"),
  sample_id = c("R1_T", "R1_N", "R2_T"),
  genotype = c("WT", "WT", "KO"),
  fastq = c("r1_t.fq.gz", "r1_n.fq.gz", "r2_t.fq.gz")
)
corrections <- tibble::tibble(
  level = c("subject", "sample"),
  id = c("R1", "R2_T"),
  column = c("genotype", "fastq"),
  value = c("KO", "r2_tumor.fq.gz"),
  reason = c("genotyping rerun on 2026-03-01", "vendor renamed the file")
)

corrected <- apply_corrections(manifest, corrections)
corrected
#> # A tibble: 3 × 5
#>   subject_id assay sample_id genotype fastq         
#>   <chr>      <chr> <chr>     <chr>    <chr>         
#> 1 R1         wes   R1_T      KO       r1_t.fq.gz    
#> 2 R1         wes   R1_N      KO       r1_n.fq.gz    
#> 3 R2         wes   R2_T      KO       r2_tumor.fq.gz
corrections_log(corrected)
#> # A tibble: 2 × 7
#>   level   id    column   old_value  new_value      reason                 n_rows
#>   <chr>   <chr> <chr>    <chr>      <chr>          <chr>                   <int>
#> 1 subject R1    genotype WT         KO             genotyping rerun on 2…      2
#> 2 sample  R2_T  fastq    r2_t.fq.gz r2_tumor.fq.gz vendor renamed the fi…      1