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scanone_np.h

/**********************************************************************
 * 
 * scanone_np.h
 *
 * copyright (c) 2001, Karl W Broman, Johns Hopkins University
 *
 * last modified Nov, 2001
 * first written Nov, 2001
 *
 * Licensed under the GNU General Public License version 2 (June, 1991)
 *
 * C functions for the R/qtl package
 *
 * These functions are for performing a non-parametric genome scan 
 * (with a single QTL model), an extension of the Kruskal-Wallis test.
 *
 * Contains: R_scanone_np, scanone_np
 *  
 **********************************************************************/

/**********************************************************************
 * 
 * R_scanone_np
 *
 * Wrapper for call from R; reorganizes genotype prob and result matrix
 * and calls scanone_np.
 * 
 **********************************************************************/

void R_scanone_np(int *n_ind, int *n_pos, int *n_gen, 
              double *genoprob, double *pheno,
              double *result);

/**********************************************************************
 * 
 * scanone_np
 *
 * Performs genotype scan using a non-parametric version of 
 * interval mapping.  (The multipoint genotype probabilities have
 * already been calculated in calc.genoprob).
 * 
 * n_ind        Number of individuals
 *
 * n_pos        Number of marker positions
 *
 * n_gen        Number of different genotypes
 *
 * Genoprob     Array of conditional genotype probabilities
 *              (indexed as Genoprob[gen][pos][ind]
 *
 * pheno        Phenotype data, as a vector of ranks
 *
 * result       Result vector of length n_pos (the lod score)
 *
 **********************************************************************/

void scanone_np(int n_ind, int n_pos, int n_gen, 
            double ***Genoprob, double *pheno,
            double *result);

/* end of scanone_np.h */

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