Mercurial > repos > melpetera > intensity_checks

comparison Intchecks/wrapper_intensity_check.R @ 0:c2c2e1be904a draft

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author melpetera
date Thu, 11 Oct 2018 05:33:19 -0400
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children 4973a2104cfd
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-1:000000000000 0:c2c2e1be904a
1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
2
3 ####################################################################
4 # WRAPPER for INTENSITY CHECK
5 #Script: Script_intensity_check_v1.R
6 #Xml: xml_intensity_check_v1.xml
7 #
8 # V1: Fold and NA
9 #
10 # Input: Data Matrix, VariableMetadata, SampleMetadata
11 # Output: VariableMetadata, Graphics (barplots and boxplots)
12 #
13 #
14 ####################################################################
15
16
17 library(batch) #necessary for parseCommandArgs function
18 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
19
20 source_local <- function(...){
21 argv <- commandArgs(trailingOnly = FALSE)
22 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
23 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
24 }
25 #Import the different functions
26 source_local("Script_intensity_check.R", "RcheckLibrary.R")
27
28
29 if(length(args) < 7){ stop("NOT enough argument !!!") }
30
31 class1 <- NULL
32 if(args$type == "One_class"){
33 class1 <- args$class1
34 }
35
36 #print args
37 cat("\n-------------------------------\nIntensity Check parameters:\n\n")
38 print(args)
39 cat("--------------------------------\n")
40
41
42 intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$type,
43 args$class_col, class1, args$variableMetadata_out, args$graphs_out)
44
45 sessionInfo()
46 cat("--------------------------------\n")
47
48 #delete the parameters to avoid the passage to the next tool in .RData image
49 rm(args)