R/scan2.R

In duytpm16/qtl2utils: Modification of QTL2 Plots

scan2 <- function(genoprobs, pheno, kinship = NULL, addcovar = NULL,
                  Xcovar = NULL, intcovar = NULL, weights = NULL, reml = TRUE,
                  model = c("normal", "binary"), cores = 1, ...){


        ### Genome scan
        if(!is.null(intcovar)){
           # Do difference between interaction and additive scan
           pca.scan <- scan1(genoprobs = genoprobs,
                             pheno = pheno,
                             kinship = K,
                             addcovar = covar,
                             cores = num_cores)

           pca.scan.int <- scan1(genoprobs = genoprobs,
                                 pheno = pheno,
                                 kinship = K,
                                 addcovar = covar,
                                 intcovar = int_covar,
                                 cores = num_cores)

           pca.scan.diff <- pca.scan.int - pca.scan

           return(list('add.scan' = pca.scan, 'int.scan' = pca.scan.int, 'diff.scan' = pca.scan.diff))

        }else{
           # Do additive scan only
           pca.scan <- scan1(genoprobs = genoprobs, pheno = pheno, kinship = K, addcovar = covar, cores = num_cores)

           return(pca.scan)
        }
}