queryEncode: query data from ENCODE by predefined criteria

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

query data from ENCODE by predefined criteria

Description

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

Usage

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"))

jianhong/enhancerHomologSearch documentation built on Nov. 4, 2024, 8:29 p.m.