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Read a Salmon Data Package

Source: R/package-helpers.R
read_salmon_datapackage.Rd

Loads a Salmon Data Package from disk. When canonical SDP CSV metadata files are present, those are treated as the source of truth. If they are missing, the function falls back to reconstructing metadata from datapackage.json for backwards compatibility with older metasalmon outputs.

Usage

read_salmon_datapackage(path)

Arguments

path

Character; path to directory containing Salmon Data Package files

Value

A list with components:

  • dataset: Dataset metadata tibble

  • tables: Table metadata tibble

  • dictionary: Dictionary tibble

  • codes: Codes tibble (if available)

  • resources: Named list of data tibbles

Examples

# Read the bundled example package without a network call.
example_path <- system.file("extdata", package = "metasalmon")
pkg <- read_salmon_datapackage(example_path)
#> ✔ Loaded Salmon Data Package from /private/var/folders/pm/twz8_z1j6_zb996w0b17bz2r0000gn/T/RtmpP4K6i1/temp_libpath110114920c408/metasalmon/extdata
names(pkg$resources)
#> [1] "nuseds_fraser_coho"