ena_get_filereport: Get file reports via ENA Portal API

In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

Get file reports via ENA Portal API

Description

Works at least with sample and run accessions.

Usage

ena_get_filereport(
  accession,
  fields = c("accession", "run_accession", "nominal_length", "read_count",
    "base_count", "library_selection", "environment_biome", "environment_feature",
    "environment_material", "instrument_model", "instrument_platform", "library_name",
    "library_strategy", "sample_accession", "sample_collection", "sampling_platform",
    "sequencing_method", "project_name"),
  base_url = "https://www.ebi.ac.uk/ena/portal/api/",
  ...
)

Arguments

accession	Sample/run accession
fields	Fields to return. Use ena_get_search_fields() to list all possible fields.
base_url	ENA API base url
...	Parameters passed to httr::GET

Details

ENA Portal API: https://www.ebi.ac.uk/ena/portal/api/

Value

data.frame

Examples

df = ena_get_filereport('ERR479486')
df = ena_get_filereport('SRS2472312')

leylabmpi/LeyLabRMisc documentation built on Nov. 3, 2022, 3:45 p.m.