FlowRepositoryR (version 1.4.0)

flowRep.submitGeneStatus: Submit information about an IMPC gene analysis results to FlowRepository.

Description

This function connects to FlowRepository via a programming interface and submits results of the analysis of a specified IMPC gene. These results shall contain information about whether the gene has been found phenodeviant. In addition, a comment may be specified, and information about whether the analysis of this gene is completed.

Usage

flowRep.submitGeneStatus(mgiGeneId, geneSymbol, isPhenodeviant,  comment=NULL, isProcessed=TRUE)

Arguments

mgiGeneId

MGI gene ID of the gene that the results are for.

geneSymbol

Gene symbol of the gene that the results are for. This shall be consistent with the MGI gene ID.

isPhenodeviant

An object of type logicle (i.e, TRUE or FALSE) indicating whether the gene has been found to couse the specimens to be phenodeviant.

comment

An optional comment about the analysis of this gene.

isProcessed

An object of type logicle (i.e, TRUE or FALSE) indicating whether the gene analysis has been completed for this gene.

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 (unknown gene)" if you try to specify a gene that is not known to FlowRepository. 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 gene needs to be found in FlowRepository, i.e., a specimen with this gene needs to be known to FlowRepository; both the MGI gene ID and the gene symbol need to match.

References

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

See Also

setFlowRepositoryCredentials, flowRep.submitImpcResults, flowRep.get

Examples

    ## This will not submit results as the public FlowRepository is not
    ## accepting those at this point.
    tryCatch(
        {
            mgiGeneId <- "geneX1"
            geneSymbol <- "gXr1"
            comment <- "This will not submit anything due to no credentials."
            flowRep.submitGeneStatus(
                mgiGeneId = mgiGeneId, 
                geneSymbol = geneSymbol, 
                isPhenodeviant = TRUE, 
                comment = comment, 
                isProcessed = TRUE)
        },
        interrupt = function(ex) { NULL; },
        error = function(ex) { NULL; }
    )