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())id: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: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:character or
NULL containing the name of this dataset.
public:logical or
NULL containing the information whether this dataset is public.
primary.researcher:character or
NULL containing the name of the primary researcher
associated with this dataset.
primary.investigator:character or
NULL containing the name of the primary investigator
associated with this dataset.
uploader:character or
NULL containing the name of the uploader of this dataset.
experiment.dates: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:character or
NULL stating the purpose of this dataset (experiment).
conclusion:character or
NULL stating the conclusion associated with this dataset
(typically conclusions reached by analyzing the data).
comments:character or
NULL stating additional comments associated with this dataset.
funding:character or NULL
stating the funding used to collect the data in this dataset.
qc.measures:character or
NULL stating the quality control measures taken in order to
ensure the quality of data in this dataset.
miflowcyt.score: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:list (of objects
of class character) enumerating keywords associated
with this dataset.
publications:list (of objects
of class character) enumerating publications associated
with this dataset. Publications are typically listed as
"PMID:12345678" or "PMCID:PMC1234567".
organizations:list of objects
of class flowRepOrganization
enumerating organizations associated with this dataset.
fcs.files:list of objects
of class fcsProxy
enumerating FCS files associated with this dataset.
attachments:list of objects
of class attachmentProxy
enumerating attachments associated with this dataset.
impc.experiments:list
enumerating IMPC experiments associated with this FlowRepository
experiment.
flowRepData.
See summary for details.
Usage:
summary(flowRepData)
localpath slots and return an updated copy
of the flowRepData object.
See download for details.
Usage:
download(flowRepData)
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 for details.
Usage:
id(flowRepData)
list of objects
of class fcsProxy
enumerating FCS files associated with this dataset.
list of objects
of class attachmentProxy
enumerating attachments associated with this dataset.
list of objects
of class flowRepOrganization
enumerating organizations associated with this dataset.
list of objects
enumerating IMPC experiments associated with this dataset.
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.
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.
flowRep.get,
download
## Obtain dataset information from FlowRepository
myDataset <- flowRep.get("FR-FCM-ZZZG")
id(myDataset)
is.downloaded(myDataset)
summary(myDataset)
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