Mercurial > repos > melpetera > intensity_checks
diff Intchecks/wrapper_intensity_check.R @ 1:4973a2104cfd draft
Uploaded
| author | melpetera |
|---|---|
| date | Wed, 05 Dec 2018 10:27:45 -0500 |
| parents | c2c2e1be904a |
| children | bdee2c2c484b |
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--- a/Intchecks/wrapper_intensity_check.R Thu Oct 11 05:33:19 2018 -0400 +++ b/Intchecks/wrapper_intensity_check.R Wed Dec 05 10:27:45 2018 -0500 @@ -1,17 +1,18 @@ #!/usr/bin/Rscript --vanilla --slave --no-site-file -#################################################################### -# WRAPPER for INTENSITY CHECK -#Script: Script_intensity_check_v1.R -#Xml: xml_intensity_check_v1.xml -# -# V1: Fold and NA -# -# Input: Data Matrix, VariableMetadata, SampleMetadata -# Output: VariableMetadata, Graphics (barplots and boxplots) -# -# -#################################################################### + +############################################################################# +# WRAPPER for INTENSITY CHECK # +# # +#Script: Script_intensity_check.R # +#Xml: xml_intensity_check.xml # +# # +# # +# Input: Data Matrix, VariableMetadata, SampleMetadata # +# Output: VariableMetadata, Graphics (barplots and boxplots) # +# # +# # +############################################################################# library(batch) #necessary for parseCommandArgs function @@ -26,21 +27,25 @@ source_local("Script_intensity_check.R", "RcheckLibrary.R") -if(length(args) < 7){ stop("NOT enough argument !!!") } +if(length(args) < 8){ stop("NOT enough argument !!!") } + class1 <- NULL +fold_frac <- NULL if(args$type == "One_class"){ class1 <- args$class1 + fold_frac <- args$fold_frac } + #print args cat("\n-------------------------------\nIntensity Check parameters:\n\n") print(args) cat("--------------------------------\n") -intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$type, - args$class_col, class1, args$variableMetadata_out, args$graphs_out) +intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$class_col, args$type, + class1, fold_frac, args$logarithm, args$variableMetadata_out, args$graphs_out) sessionInfo() cat("--------------------------------\n")