plot_GeneSymbol_Meth450: plot_GeneSymbol_Meth450
In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description Usage Arguments Value Examples

Plots stripcharts and replicate diagrams for the given arguments. Also plots heatmaps for probes. Uses the gene symbol in the argument to look up probes and plots for those probes.

1	plot_GeneSymbol_Meth450(theGene, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag = FALSE, theUseDeltaFlag = FALSE, theReplicateFlag=FALSE)

`theGene`	The gene symbol to plot which corresponds to an id from the appropriate getNames_ function and maps to one or more probes.
`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 (theGene, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", 
    theVerboseFlag = FALSE, theUseDeltaFlag = FALSE) 
{
    plot_fromGene_internal(theGene, theOutputDir, theZipFile, 
        theMapGeneToProbesFunction = getNames_ProbeFromGeneSymbol_Meth450, 
        theReadProbeFunction = getMetadata_Probe_Meth450, theReadGeneFunction = getData_Probe_Meth450, 
        theDataType = "Meth450", theDataTypeLabel = "Beta Value", 
        theVerboseFlag = theVerboseFlag, theUseDeltaFlag = theUseDeltaFlag)
  }