getContrast: getContrast
In MD-Anderson-Bioinformatics/GeneSurvey: MD Anderson Gene Survey

Description Usage Arguments Details Value Examples

Give two genes and two assays (platforms), match up the data by sample/patient, calculate the correlations, print scatterplots, and return the correlations and data used for them.

getContrast(theOutdir, theGene1, theAssay1, theGene2, theAssay2,
theZipFile="/geneSurveyData/GeneSurvey.zip",
theMethod = "spearman", theUse = "pairwise.complete.obs",
theUseDeltaFlag = FALSE, theRemoveDupFlag = TRUE, theVerboseFlag = FALSE)

`theOutdir`	Directory to which to write the diagrams
`theGene1`	Gene or gene equivalent, which should match the gene equivalents for the matching assay
`theAssay1`	One of Meth450, Meth27, miRNASeq, SNP6, RnaSeq, or RnaSeq2
`theGene2`	Gene or gene equivalent, which should match the gene equivalents for the matching assay
`theAssay2`	One of Meth450, Meth27, miRNASeq, SNP6, RnaSeq, or RnaSeq2
`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 "/geneSurveyData/GeneSurvey.zip".
`theMethod`	Default: "spearman". Value for the method argument to cor: "pearson", "kendall", "spearman"
`theUse`	Default: "pairwise.complete.obs". Value for the use argument to cor: "everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs"
`theUseDeltaFlag`	Default: FALSE. A flag indicating to use the differences in value between tumor and normal samples.
`theRemoveDupFlag`	Default: FALSE. Remove the duplicate barcodes from the same control samples used in different diseases.
`theVerboseFlag`	Default: FALSE. TRUE means write all output, which can be very verbose.

Give two genes and two assays (platforms), match up the data by sample/patient, calculate the correlations, print scatterplots, and return the corrrelations and data used for them.

A list of sublists (with names()) corresponding to "Overall" and then the valid disease types. Each sublist has [[1]] the results from calling cor, [[2]] the first data set used in calling cor, and [[3]] the second data set used in calling cor. Sample ids are barcodes reduced to 19 characters unless delta data is used, in which case it is the patient id (12 characters).