HCABrowser: Browse the HCA

In Bioconductor/HCABrowser: Browse the Human Cell Atlas data portal

Description

Use HCABrowser() to create an object to connect with the Human Cell Atlas Data Coordination Platform Data Storage System (HCA DCP DSS).

searchBundles() searches the HCA DCP DSS for bundles matching the filters applied to the HCA object.

Usage

HCABrowser(
  host = "dss.data.humancellatlas.org",
  api_url = "https://dss.data.humancellatlas.org/v1/swagger.json",
  per_page = 10,
  authenticate = FALSE
)

getEsQuery(x)

undoEsQuery(x, n = 1L)

resetEsQuery(x)

searchBundles(
  x,
  output_format = c("summary", "raw"),
  replica = c("aws", "gcp"),
  per_page = 100L
)

## S4 method for signature 'HCABrowser'
show(object)

Arguments

host	character(1) path to hca-dcp server
api_url	character(1) path to hca-dcp api file
per_page	numeric(1). Max number of results to return per page.
authenticate	logical(1) authenticate? required for actions that update the HCA data repostiory (rare).
x	An HCABrowser object
n	integer(1) the number of filter queries to undo
output_format	character(1). Specifies the output format. Either "summary" or "raw". The default format, "summary", is a list of UUIDs for bundles that match the query. Set this parameter to "raw" to get the verbatim JSON metadata for bundles that match the query.
replica	character(1). A replica to fetch form. Can either be set to "aws" or "gcp". DEFAULT is "aws".
object	An HCAbrowser object to show

Details

getEsQuery(), undoEsQuery(), and resetEsQuery() retrieve, remove the most recent, or remove all filters added to an HCABrowser object via filter().

searchBundles() can return summary or raw results. summary results include the bundle_fqid (unique identifier) and bundle_url (location of a JSON file with complete bundle information). Up to 500 summary or 10 raw results can be returned per query; use nextResults() to 'page' through subsequent bundles.

Value

HCABrowser() returns an object representing the connection to the HCA DCP DSS.

getEsQuery() returns a JSON object representing the elastic search query formed by application of filter()andselect()' to an HCABrowser object.

undoEsQuery() returns an HCABrowser object with n fewer queries.

'resetEsQuery()' returns an HCABrowser object with no queries.

Author(s)

Daniel Van Twisk

Examples

HCABrowser()

hca <-
    HCABrowser() %>%
    filter(organ.text == brain) %>%
    filter(organ.text == heart)

hca

str(getEsQuery(hca))

hca %>%
    undoEsQuery()

hca %>%
    resetEsQuery()

searchBundles(HCABrowser(), per_page = 10L) # All records!
HCABrowser() %>%
    filter(files.specimen_from_organism_json.organ.text == "brain") %>%
    searchBundles() %>%
    as_tibble()

Bioconductor/HCABrowser documentation built on Feb. 10, 2021, 12:51 p.m.