plotAssays: plotAssays

Description Usage Arguments Details Value Examples

View source: R/plotAssays.R

Description

Plot data from different assays against each other

Usage

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

Arguments

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.

Details

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.

Value

returns vector of file names created.

Examples

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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.