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lib/Genome/Model/Tools/Music/ClinicalCorrelation.pm.R  view on Meta::CPAN

    # x.file="*" if x.file already merged into y.file 

    ### about x.names
    # x.names="*" will use all column names in x.file as x variable names
    # or you can define it in the format x.names="gene1|gene2|gene3"
    # self-defined x.names have to be found in column names of y.file and/or x.file  

    #################### myglm fuction ##############
    myglm=function(z,trait,variant,covar=NA,ytype) {
        if (nchar(covar)==0 | is.na(covar) | is.null(covar)) { 
            model=formula(paste(trait,"~",variant)) 
        } else {
            model=formula(paste(trait,"~",variant,"+",covar))
        }
        if (ytype=="B") fit=glm(formula=model,data=z,family=binomial(link = "logit"))
        if (ytype=="Q") fit=glm(formula=model,data=z,family=gaussian(link = "identity"))
        fit
    }
    #################################################


    ### data input #####
    read.table(model.file,colClasses="character",na.strings = c("","NA"),sep="\t",header=T)->md
    read.table(y.file,na.strings = c("","NA"),sep="\t",header=T)->y
    if (x.names!="*") x.names=strsplit(x.names,split="[|]")[[1]]

lib/Genome/Model/Tools/Music/Plot/MutationRelation.pm.R  view on Meta::CPAN

# Fetch command line arguments
args = commandArgs();
input_matrix = as.character(args[4]);
genes_to_plot = as.character(args[5]);
output_pdf = as.character(args[6]);
preserveGeneOrder = as.numeric(as.character(args[7]));

sort.data.frame <- function( x, by ) {
    if(by[[1]] != "~")
        stop("Argument 'by' must be a one-sided formula.")

    ## Make the formula into character and remove spaces
    formc <- as.character(by[2])
    formc <- gsub(" ", "", formc)
    ## If the first character is not + or -, add +
    if(!is.element(substring(formc, 1, 1), c("+", "-")))
        formc <- paste("+", formc, sep = "")

    ## Extract the variables from the formula
    vars <- unlist(strsplit(formc, "[\\+\\-]"))
    vars <- vars[vars != ""] # Remove any extra "" terms

    ## Build a list of arguments to pass to "order" function
    calllist <- list()
    pos <- 1 # Position of + or -
    for(i in 1:length(vars)){
        varsign <- substring(formc, pos, pos)
        pos <- pos + 1 + nchar(vars[i])
        if(is.factor(x[, vars[i]])){