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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ##---- 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)
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.