R/classes.R

In syounkin/LD-LASSO: LD LASSO Regression for SNP Association Study (Methods and Classes)

setClassUnion("numericOrNULL", c("numeric", "NULL"))

setClass( "ldlasso", representation(
                                    geno = "matrix",
                                    pheno = "integer",
                                    s1 = "numericOrNULL",
                                    s2 = "numeric",
                                    r2 = "numeric",
                                    beta = "numeric",
                                    OR = "numeric",
                                    logOR.norm = "numeric",
                                    var = "numeric",
                                    maf.case = "numeric",
                                    maf.con = "numeric",
                                    maf.tot = "numeric",
                                    X.case = "matrix",
                                    X.con = "matrix",
                                    n.case = "numeric",
                                    n.con = "numeric"
                                    )
         )

ldlasso =
# an ldlasso object with genotype matrix (subjects by SNPs) and phenotype vector
function( geno, pheno, s1, s2, r2 )
{
  geno = as( geno, "matrix" )
  pheno = as( pheno, "integer" )
  logOR.obj <- logOR( geno, pheno )
  if( nrow( geno) != length(pheno) )
    stop( "The number of rows in geno should equal the length of pheno" )
  if(is.null(colnames(geno)))
     colnames(geno) <- paste( "SNP", 1:ncol(geno), sep = "" )
  if(is.null(rownames(geno)))
     rownames(geno) <- paste( "sub", 1:nrow(geno), sep = "" )
  new( "ldlasso",
      geno = geno,
      pheno = pheno,
      s1 = s1,
      s2 = s2,
      r2 = r2,
      OR = logOR.obj$OR,
      logOR.norm = logOR.obj$y,
      var = logOR.obj$var_y,
      maf.case = logOR.obj$f2,
      maf.con = logOR.obj$f1,
      maf.tot = logOR.obj$f0,
      X.case = logOR.obj$X2,
      X.con = logOR.obj$X1,
      n.case = logOR.obj$n1,
      n.con = logOR.obj$n0
      )
}