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

Description Usage Arguments Details Value Examples

Plot data from different assays against each other

plotAssays(theGene1, theGene2, theAssay1, theAssay2, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theUseDeltaFlag = FALSE, theRemoveDupFlag = TRUE, theVerboseFlag = FALSE)

`theGene1`	Gene equivalent for first axis. A string used to form the title and file name for the images. This should be the gene equivalent being plotted.
`theGene2`	Gene equivalent for second axis. A string used to form the title and file name for the images. This should be the gene equivalent being plotted.
`theAssay1`	Platform/assay for first axis. A string, one of Mutations, RnaSeq2, RnaSeq, SNP6, Meth450, Meth27, miRNASeq.
`theAssay2`	Platform/assay for first axis. A string, one of Mutations, RnaSeq2, RnaSeq, SNP6, Meth450, Meth27, miRNASeq.
`theOutputDir`	Directory in which to create the output
`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".
`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.

Creates points plots of one gene-equivalent plus platform-assay against another. There will be an ALL plot, with all disease types on one plot, and then plots for each disease type separately.

returns vector of file names created.

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#plotAssays("TP53", "TP53", "RnaSeq", "SNP6", '/rsrch1/bcb/batcheffects/DEV/GeneSurvey/output/RnaSeq_SNP6')
#plotAssays("TP53", "cg00807143", "RnaSeq2", "Meth450", '/rsrch1/bcb/batcheffects/DEV/GeneSurvey/output/RnaSeq2_Meth450')
#plotAssays("hsa-mir-891a.MIMAT0004902", "cg22175811", "miRNASeq", "Meth27", '/rsrch1/bcb/batcheffects/DEV/GeneSurvey/output/RnaSeq2_Meth27')

GeneSurvey/TCGAGeneReport documentation built on May 6, 2019, 6:27 p.m.