comparison Intchecks/Script_intensity_check.R @ 6:ec75de7f1e08 draft default tip

Uploaded

5:a31f3f802b2b

  DM.name <- "DM_NA.tabular"
  SM.name <- "SM_NA.tabular"
  VM.name <- "vM_NA.tabular"
  method <- "one_class"
  chosen.stat <- "mean,sd,quartile,decile,NA" 
  class.col <- "2" 
  test.fold <- "Yes" 
  class1 <- "Pools"
  fold.frac <- "Top"
  logarithm <- "log10"
  VM.output <- "new_VM.txt"

    test.fold <- "No"
  }


  if(method != "no_class"){
    
    class.col <- colnames(SM)[as.numeric(class.col)]
  
    if(!(class.col %in% colnames(SM))){
      stop("\n- - - - - - - - -\n", "The column ",class.col, " is not a part of the specify sample Metadata","\n- - - - - - - - -\n")
    }
  
    c_class <- SM[,class.col]
    c_class <- as.factor(c_class)
    nb_class <- nlevels(c_class)
    classnames <- levels(c_class)
  
    if((nb_class < 2)&&(test.fold=="Yes")){
      err.1class <- c("\n The column",class.col, "contains only one class, fold calculation could not be executed. \n")
      cat(err.1class)  
    }
  
    if((nb_class > (nrow(SM))/3)&&(method == "each_class")){
      class.err <- c("\n There are too many classes, think about reducing the number of classes and excluding those

  
    if(method == "one_class"){  
      if(!(class1 %in% classnames)){
        list.class1 <- c("\n Classes:",classnames,"\n")
        cat(list.class1)
        err.class1 <- c("The class ",class1, " does not appear in the column ", class.col)
        stop("\n- - - - - - - - -\n", err.class1,"\n- - - - - - - - -\n")
      }
  
      #If method is "one_class", change others classes in "other"
      for(i in 1:length(c_class)){

6:ec75de7f1e08

  DM.name <- "DM_NA.tabular"
  SM.name <- "SM_NA.tabular"
  VM.name <- "vM_NA.tabular"
  method <- "one_class"
  chosen.stat <- "mean,sd,quartile,decile,NA" 
  class.col <- "uv" 
  test.fold <- "Yes" 
  class1 <- "Pools"
  fold.frac <- "Top"
  logarithm <- "log10"
  VM.output <- "new_VM.txt"

    test.fold <- "No"
  }


  if(method != "no_class"){
  
    if(!(class.col %in% colnames(SM))){
      stop("\n- - - - - - - - -\n", "The ",class.col, " column is not found in the specified sample metadata file.","\n- - - - - - - - -\n")
    }
  
    c_class <- SM[,class.col]
    c_class <- as.factor(c_class)
    nb_class <- nlevels(c_class)
    classnames <- levels(c_class)
  
    if((nb_class < 2)&&(test.fold=="Yes")){
      err.1class <- c("\n The ",class.col, " column contains only one class, fold calculation could not be executed. \n")
      cat(err.1class)  
    }
  
    if((nb_class > (nrow(SM))/3)&&(method == "each_class")){
      class.err <- c("\n There are too many classes, think about reducing the number of classes and excluding those

  
    if(method == "one_class"){  
      if(!(class1 %in% classnames)){
        list.class1 <- c("\n Classes:",classnames,"\n")
        cat(list.class1)
        err.class1 <- c("The ",class1, " class does not appear in the ",class.col," column.")
        stop("\n- - - - - - - - -\n", err.class1,"\n- - - - - - - - -\n")
      }
  
      #If method is "one_class", change others classes in "other"
      for(i in 1:length(c_class)){