
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_CorrelateExpressionVsMethylation/broadinstitute.org/cancer.genome.analysis/00332/102/ExprMeth.R")
> result <- gdacExprMeth("-m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/THYM-TP/11493998/THYM-TP.meth.by_min_expr_corr.data.txt", "-e/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THYM-TP/11493749/THYM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-cspearman", "-bTHYM-TP", "-n/xchip/tcga/Tools/Nozzle/v1.current")

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_CorrelateExpressionVsMethylation/broadinstitute.org/cancer.genome.analysis/00332/102/ExprMeth.R")
> result <- gdacExprMeth("-m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/THYM-TP/11493998/THYM-TP.meth.by_min_expr_corr.data.txt", "-e/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THYM-TP/11493749/THYM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt", "-cspearman", "-bTHYM-TP", "-n/xchip/tcga/Tools/Nozzle/v1.current")
There were 50 or more warnings (use warnings() to see the first 50)
> q(save="no")
