'flowRepData': a class for storing metadata about a FlowRepository dataset

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Description

This class represents the metadata (i.e., information about) a dataset stored in FlowRepository.

Details

Objects of class flowRepData can be used to hold information about a FlowRepository dataset. This includes the FlowRepository dataset identifier, name, primary researcher, investigator and uploader, information about the purpose, conclusions, comments and funding, experiment dates, QC measures, MIFlowCyt score, keywords, organizations, publications, list of FCS file names and attachment names, and whether or not it is a public dataset. Using this objects, FCS files and attachments can be easily downloaded to your local file system. See the download method.

Creating Objects

To create a flowRepData directly from an FlowRepository, use function flowRep.get. This is the recommended and safest way of object creation, since flowRep.get will perform basic quality checks and populate all the slots accordingly. Unless you know exactly what you are doing, creating objects using new or the constructor (as described below) is discouraged.

Objects can be created using
new("flowRepData",
id = ...., Object of class character
public.url = ...., Object of class character or NULL
name = ...., Object of class character or NULL
public = ...., Object of class logical or NULL
primary.researcher = ...., Object of class character or NULL
primary.investigator = ...., Object of class character or NULL
uploader = ...., Object of class character or NULL
experiment.dates = ...., Object of class character or NULL
purpose = ...., Object of class character or NULL
conclusion = ...., Object of class character or NULL
comments = ...., Object of class character or NULL
funding = ...., Object of class character or NULL
qc.measures = ...., Object of class character or NULL
miflowcyt.score = ...., Object of class numeric or NULL
keywords = ...., Object of class list
publications = ...., Object of class list
organizations = ...., Object of class list
fcs.files = ...., Object of class list
attachments = ...., Object of class list
impc.experiments = ...., Object of class list
)

or the constructor flowRepData, with mandatory argument id and optional arguments public.url, name, public, primary.researcher, primary.investigator, uploader, experiment.dates, purpose, conclusion, comments, funding, qc.measures, miflowcyt.score, keywords, publications, organizations, fcs.files, attachments and impc.experiments.

flowRepData(id, public.url=NULL, name=NULL, public=NULL,
primary.researcher=NULL, primary.investigator=NULL,
uploader=NULL, experiment.dates=NULL,
purpose=NULL, conclusion=NULL, comments=NULL,
funding=NULL, qc.measures=NULL, miflowcyt.score=NULL,
keywords=list(), publications=list(), organizations=list(),
fcs.files=list(), attachments=list(), impc.experiments=list())

Slots

id:

Object of class character containing the FlowRepository identified of the dataset. These identifiers are typically in the form of FR-FCM-xxxx where xxxx represents 4 alphanumeric characters.

public.url:

Object of class character or NULL containing the public URL of this dataset. This will commonly be in the form of https://flowrepository.org/id/identifier, where identifier is the FlowRepository identified of the dataset.

name:

Object of class character or NULL containing the name of this dataset.

public:

Object of class logical or NULL containing the information whether this dataset is public.

primary.researcher:

Object of class character or NULL containing the name of the primary researcher associated with this dataset.

primary.investigator:

Object of class character or NULL containing the name of the primary investigator associated with this dataset.

uploader:

Object of class character or NULL containing the name of the uploader of this dataset.

experiment.dates:

Object of class character or NULL containing the dates associated with this dataset. Typically, there will be two dates associated with the dataset, the first one for the start of the experiment, the second one for the end of the experiment. A single date indicates the start of an experiment that may still be ongoing. The dates shall be encoded as "YYYY-MM-DD".

purpose:

Object of class character or NULL stating the purpose of this dataset (experiment).

conclusion:

Object of class character or NULL stating the conclusion associated with this dataset (typically conclusions reached by analyzing the data).

comments:

Object of class character or NULL stating additional comments associated with this dataset.

funding:

Object of class character or NULL stating the funding used to collect the data in this dataset.

qc.measures:

Object of class character or NULL stating the quality control measures taken in order to ensure the quality of data in this dataset.

miflowcyt.score:

Object of class numeric or NULL stating the MIFlowCyt compliance score of this experiment. MIFlowCyt is the Minimum Information about a Flow Cytometry Experiment - an ISAC Recommendation listing the minimum information that shall be provided as annotation of flow cytometry datasets. The MIFlowCyt compliance score is a value between 0 and 100 percent indicating the level of compliance with MIFlowCyt. Details about how FlowRepository calculates this score ara available here: http://flowrepository.org/quick_start_guide#MIFlowCytScoreReport

keywords:

Object of class list (of objects of class character) enumerating keywords associated with this dataset.

publications:

Object of class list (of objects of class character) enumerating publications associated with this dataset. Publications are typically listed as "PMID:12345678" or "PMCID:PMC1234567".

organizations:

Object of class list of objects of class flowRepOrganization enumerating organizations associated with this dataset.

fcs.files:

Object of class list of objects of class fcsProxy enumerating FCS files associated with this dataset.

attachments:

Object of class list of objects of class attachmentProxy enumerating attachments associated with this dataset.

impc.experiments:

Object of class list enumerating IMPC experiments associated with this FlowRepository experiment.

Methods

There are separate documentation pages for some of the methods listed here which may be consulted for more details.

summary

Print a basic summary about a flowRepData. See summary for details. Usage: summary(flowRepData)

download

Download all the referenced FCS files and attachments, fill out their localpath slots and return an updated copy of the flowRepData object. See download for details. Usage: download(flowRepData)

is.downloaded

Return TRUE if all FCS files and attachments referenced from this flowRepData object are downloaded to your local file system. This is determined by the localpath slot of the fileProxy objects in the fcs.files list and attachments list. No other checks are performed. See is.downloaded for details. Usage: is.downloaded(flowRepData)

id

Return the character vector representing the identifier to the FlowRepository dataset. See id for details. Usage: id(flowRepData)

fcs.files

Return an object of class list of objects of class fcsProxy enumerating FCS files associated with this dataset.

attachments

Return an object of class list of objects of class attachmentProxy enumerating attachments associated with this dataset.

organizations

Return an object of class list of objects of class flowRepOrganization enumerating organizations associated with this dataset.

impc.experiments

Return an object of class list of objects enumerating IMPC experiments associated with this dataset.

impcResultsCopy

Return an object of class list with a copy of IMPC analysis results. See impcResultsCopy for details. Usage: impcResultsCopy(flowRepData, experimentIndex, resultIndex) The result is a copy of what can typically be found in flowRepData@impc.experiments[[experimentIndex]]$ impc_parameter_sets[[resultIndex]] but without the updated_at, created_at, id, gated_by, gated_by_id, and impc_experiment_id.

Author(s)

Josef Spidlen

See Also

flowRep.get, download

Examples

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    ## Obtain dataset information from FlowRepository
    myDataset <- flowRep.get("FR-FCM-ZZZG")
    id(myDataset)
    is.downloaded(myDataset)
    summary(myDataset)

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