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Write a manifest or a cohort's tables to a delimited file

Source: R/io.R
write_manifest.Rd

Joins a cohort's (or a validate_manifest() result's) sample_map and subject_tbl back into one long-format manifest and writes it to a CSV, TSV, or other delimited file.

Usage

write_manifest(x, path, delim = NULL)

Arguments

x

A Cohort object, or the list returned by validate_manifest() or read_manifest() (anything with subject_tbl and sample_map).

path

Output file path. The delimiter is chosen from the extension unless delim is given.

delim

Optional character scalar overriding delimiter detection.

Value

The written manifest tibble, invisibly.

Details

Columns are ordered subject_id, then the other subject-level columns, then the sample-level columns (assay, sample_id, role, and any extra ones). A missing value is written as an empty field.

See also

read_manifest(), validate_manifest(), cohort_save()

Examples

manifest <- data.frame(
  subject_id = "R1",
  species = "rat",
  assay = "wes",
  sample_id = "T1",
  role = "tumor",
  stringsAsFactors = FALSE
)
parsed <- validate_manifest(manifest)

out <- tempfile(fileext = ".csv")
write_manifest(parsed, out)
readLines(out)
#> [1] "subject_id,species,assay,sample_id,role"
#> [2] "R1,rat,wes,T1,tumor"