Mercurial > repos > melpetera > intensity_checks

comparison Intchecks/wrapper_intensity_check.R @ 4:49c36c54e0cf draft

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Uploaded
author melpetera
date Fri, 03 Jan 2020 11:09:05 -0500
parents bdee2c2c484b
children ec75de7f1e08
comparison
equal deleted inserted replaced
3:bdee2c2c484b 4:49c36c54e0cf
27 source_local("Script_intensity_check.R", "RcheckLibrary.R") 27 source_local("Script_intensity_check.R", "RcheckLibrary.R")
28 28
29 29
30 if(length(args) < 7){ stop("NOT enough argument !!!") } 30 if(length(args) < 7){ stop("NOT enough argument !!!") }
31 31
32 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
33 '\n\n--------------------------------------------------------------------',
34 '\nIntensity Check parameters:\n\n')
35 print(args)
36 cat('--------------------------------------------------------------------\n\n')
37
32 class_col <- NULL 38 class_col <- NULL
33 test_fold <- NULL 39 test_fold <- NULL
34 class1 <- NULL 40 class1 <- NULL
35 fold_frac <- NULL 41 fold_frac <- NULL
36 logarithm <- NULL 42 logarithm <- NULL
53 59
54 err_no_option <- NULL 60 err_no_option <- NULL
55 61
56 if(((args$method == "no_class")&&(args$chosen_stat == "None"))|| 62 if(((args$method == "no_class")&&(args$chosen_stat == "None"))||
57 ((args$method != "no_class") && (args$chosen_stat == "None") && (test_fold == "No"))){ 63 ((args$method != "no_class") && (args$chosen_stat == "None") && (test_fold == "No"))){
58 err_no_option<- "You did not select any computational option. Program could not be executed." 64 err_no_option<- "You did not select any computational option. Program can not be executed."
59 stop("\n- - - - - - - - -\n",err_no_option,"\n- - - - - - - - -\n") 65 stop("\n- - - - - - - - -\n",err_no_option,"\n- - - - - - - - -\n")
60 } 66 }
61 67
62
63 #print args
64 cat("\n-------------------------------\nIntensity Check parameters:\n\n")
65 print(args)
66 cat("--------------------------------\n")
67 68
68 if(is.null(err_no_option)){ 69 if(is.null(err_no_option)){
69 70
70 intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$method, args$chosen_stat, 71 intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$method, args$chosen_stat,
71 class_col, test_fold, class1, fold_frac, logarithm, args$variableMetadata_out, args$graphs_out) 72 class_col, test_fold, class1, fold_frac, logarithm, args$variableMetadata_out, args$graphs_out)
72 } 73 }
73 74
75
76 cat('\n--------------------------------------------------------------------',
77 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
74 sessionInfo() 78 sessionInfo()
75 cat("--------------------------------\n") 79 cat('--------------------------------------------------------------------\n',
80 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
81
76 82
77 #delete the parameters to avoid the passage to the next tool in .RData image 83 #delete the parameters to avoid the passage to the next tool in .RData image
78 rm(args) 84 rm(args)