List identifiers of datasets available in FlowRepository

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Description

This function connects to FlowRepository (flowrepository.org) via an XML-based API and retrieves a vector of identifiers of available datasets.

Usage

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    flowRep.ls(
        include.private = FALSE, 
        impc.only = FALSE,
        impc.unanalyzed.only = FALSE,
        impc.centre = NULL, 
        impc.date.from = NULL, impc.date.to = NULL,
        impc.specimen.geneKO.mgiId=NULL,
        impc.specimen.geneKO.geneSymbol=NULL,
        impc.specimen.baseline=NULL,
        impc.specimen.minCount=NULL
    )

Arguments

include.private

Whether to include private experiments in the list. This only works if credentials to access FlowRepository have been provided. By default, only public experiments will be listed.

impc.only

Whether to return only datasets that are related to IMPC experiments and IMPC specimen.

impc.unanalyzed.only

Whether to return only datasets that are related to an IMPC experiment and that do not have any automated analysis results associated with.

impc.centre

Whether to return only datasets that are related to an IMPC experiment performed by a specified IMPC centre. If this is not NULL then it shall be an ILAR code of a known IMPC centre; see also listKnownIlarCodes. The impc.only will be set to TRUE automatically if impc.centre is provided.

impc.date.from

Whether to return only datasets that are related to an IMPC experiment performed on or after the specified date. If this is not NULL then it shall be a value of the Date class, e.g., as.Date("2015-11-24", "%Y-%m-%d"). The impc.date.to will be set to TRUE automatically if impc.centre is provided.

impc.date.to

Whether to return only datasets that are related to an IMPC experiment performed on or before the specified date. If this is not NULL then it shall be a value of the Date class, e.g., as.Date("2015-11-24", "%Y-%m-%d"). The impc.date.to will be set to TRUE automatically if impc.centre is provided.

impc.specimen.geneKO.mgiId

Whether to return only datasets related to an IMPC experiment that involves a specimen with a specified gene knockout (KO). In this argument, the KO gene is referenced by its MGI gene id. The impc.date.to will be set to TRUE automatically if impc.centre is provided.

impc.specimen.geneKO.geneSymbol

Whether to return only datasets related to an IMPC experiment that involves a specimen with a specified gene knockout (KO). In this argument, the KO gene is referenced by its gene symbol. The impc.date.to will be set to TRUE automatically if impc.centre is provided.

impc.specimen.baseline

Whether to return only datasets related to an IMPC experiment that involves a specimen with a specified boolean baseline attribute, the value of which shall match the value of this argument. That means, if impc.specimen.baseline is set to TRUE then only IMPC specimen marked as baseline will be considered. If impc.specimen.baseline is set to FALSE then only IMPC specimen that are not marked as baseline will be considered. If impc.specimen.baseline is left as NULL then both baseline and not baseline specimen will be considered. The impc.date.to will be set to TRUE automatically if impc.centre is provided.

impc.specimen.minCount

Whether to return only datasets related to IMPC experiments that together involve at least the specified minimum number of specimen. The impc.date.to will be set to TRUE automatically if impc.centre is provided.

Details

An HTTP GET request retrieves an XML from FlowRepository, and this XML is parsed to extract the list of identifiers of public experiments.

Value

A vector of objects of class character containing strings with FlowRepository dataset identifiers available.

Author(s)

Josef Spidlen

References

Spidlen Josef. FlowRepository Resources for Developers.
http://flowrepository.org/developers

See Also

flowRep.get, setFlowRepositoryCredentials listKnownIlarCodes ilarCodeDescription

Examples

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