FlowRepositoryR (version 1.4.0)

flowRep.submitImpcResults: Submit IMPC data analysis results to FlowRepository.

Description

This function connects to FlowRepository via a programming interface and submits results of the analysis of a specified IMPC experiment. These results shall contain counts for IMPC defined cell populations.

Usage

flowRep.submitImpcResults(gatedByIlar, impcExpId, results, final=TRUE)

Arguments

gatedByIlar

The ILAR code of the laboratory that perforned the data analysis. See http://dels.nas.edu/global/ilar/Lab-Codes for more info about ILAR codes. The laboratory needs to be listed among those allowed to submit IMPC data analysis results to FlowRepository

impcExpId

The IMPC experiment id of the experiment that the results are being submitted for.

results

The results that are being submitted. This shall be a list of objects with names corresponding to IMPC parameter codes as defined in https://www.mousephenotype.org/impress/protocol/174/7 (e.g., IMPC_IMM_011_001 to state the number of CD4 NKT cells in IMPC panel A). See also impcResultsCopy.

final

Whether the results being submitted shall be considered to be the final results. This should be set to TRUE only if a final (complete) set of results is being submitted (i.e., results for both panels are there). If you are submitting intermediate results, such as results for one of the panel only, you should set this to FALSE and then you can use FlowRepository to store your intermediate results now with the intention to add to those later.

Value

A list of 2 objects named response and status. The response contains a text of the response from the server, such as "Results submitted." if the results have been accepted. The status will contain the HTTP status code of the response, such as "200 OK" if everything was successful. An example if an unacceptable response is "Bad results (impc_imm_049_001 out of range, value should be between 0 and 100)" if you try to specify the percentage of live gated events in Panel B outside of the 0-100 range. The "400 Bad Request" status is to be expected in this case.

Details

An HTTP POST request sends the results to FlowRepository. You need to have your credentials set (see setFlowRepositoryCredentials) and you as the user need to have permissions to subnit IMPC data analysis results. In addition, the laboratory needs to be listed among those allowed to submit IMPC data analysis results to FlowRepository. You may need to contact your FlowRepository administrators if you are not allowed to submit IMPC results. In addition, note that at this point, the public FlowRepository (available at FlowRepository.org) does not contain IMPC data and is not accepting these sorts of results. There are private FlowRepository instances only for IMPC data at this point. Also, note that some basic consistency checks are in place and FlowRepository may refuse results that appear to be wrong.

References

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

See Also

setFlowRepositoryCredentials, impcResultsCopy, flowRep.submitGeneStatus, flowRep.get

Examples

    ## This will not submit results as the public FlowRepository is not
    ## accepting those at this point, "H" is probably not allowed to submit
    ## IMPC results, "impcEx0001" is a made up IMPC experiment ID,
    ## and finally, the user did not set her credentials...
    tryCatch(
        {
            centreILAR <- "H"
            expId <- "impcEx0001"
            results <- list(
                impc_imm_001_001 = 0.12, 
                impc_imm_026_001 = 1000000, 
                impc_imm_002_001 = 87.345, 
                impc_imm_027_001 = 1000000, 
                impc_imm_049_001 = 91.567, 
                impc_imm_002_001 = 543213)
            flowRep.submitImpcResults(centreILAR, expId, results)
        },
        interrupt = function(ex) { NULL; },
        error = function(ex) { NULL; }
    )