query data from ENCODE by predefined criteria

Search ENCODE data by querying the ENCODE Portal using its REST API.

queryEncode(
  exactMatch,
  partialMatch = character(0),
  API_url = "https://www.encodeproject.org/search/",
  ...
)

Arguments

exactMatch

character. Exact-match keywords refer to search results that perfectly match all the keywords in the search query, exactly as entered. It is a named character vector. The names will be the keys and characters will be the values for search.

partialMatch

character. Partial-match refer to search results that contain the search query. It is a named character vector. The names will be the keys and characters will be the values for search. The value starting from '!' indicates logical negation(NOT). The value starting from '>', '>=', '<', '==', '<=' indicates string comparison.

API_url

character. The ENCODE REST API url.

...

Not used.

Value

A list of search results

Examples

res <- queryEncode(
 exactMatch=c(
  target.label="H3K4me1",
  replicates.library.biosample.donor.organism.scientific_name="Homo sapiens",
  assembly="GRCh38",
  assay_term_name="ChIP-seq"),
  partialMatch=c(biosample_summary="heart"))