plot_Probe_Meth27: plot_Probe_Meth27
In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description Usage Arguments Value Examples

Plots stripcharts and replicate diagrams for the given arguments.

1	plot_Probe_Meth27(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag = FALSE, theUseDeltaFlag = FALSE, theReplicateFlag=FALSE)

`theGeneEq`	The probe to plot which corresponds to an id from the appropriate getNames_ function.
`theOutputDir`	Directory to which to write files. Directory will be created if needed/possible.
`theZipFile`	Default: For DQS Servers. If you are on a server where the GENE_REPORT directory is on a different path, you can pass in a value to override the default of "/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip".
`theVerboseFlag`	Default: FALSE. TRUE means write all output, which can be very verbose.
`theUseDeltaFlag`	Default: FALSE. A flag indicating to use the differences in value between tumor and normal samples.
`theReplicateFlag`	Default: FALSE. A flag indicating to write the replicate plots.

A list of files output.

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", 
    theVerboseFlag = FALSE, theUseDeltaFlag = FALSE) 
{
    myProbe <- getMetadata_Probe_Meth27(theGeneEq, file.path(theZipFile, 
        "data"))
    myGeneData <- NULL
    myBarcodeDiseases <- NULL
    myBarcodeSampleType <- NULL
    myTag <- ""
    if (TRUE == theUseDeltaFlag) {
        myTag <- "Delta"
    }
    myGeneData <- getData_Probe_Meth27(theGeneEq, theZipFile, 
        theVerboseFlag = theVerboseFlag, theUseDeltaFlag = theUseDeltaFlag)
    myBarcodeDiseases <- getMetadataPop_BarcodeDisease(file.path(theZipFile, 
        "data"), theVerboseFlag = theVerboseFlag)
    myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(file.path(theZipFile, 
        "data"), theVerboseFlag = theVerboseFlag)
    geneEqPre <- paste(padChromosomeName(myProbe@mChromosome), 
        "-", myProbe@mProbeLocation, "-", sep = "")
    plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases, 
        myBarcodeSampleType, "Meth27", "Beta Value", theVerboseFlag = theVerboseFlag, 
        theTag = myTag, theGeneEqPre = geneEqPre)
  }