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/**********************************************************************
*
* scantwo_binary_hk.h
*
* copyright (c) 2010, Karl W Broman
*
* last modified Jun, 2010
* first written Jun, 2010
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License,
* version 3, as published by the Free Software Foundation.
*
* This program is distributed in the hope that it will be useful,
* but without any warranty; without even the implied warranty of
* merchantability or fitness for a particular purpose. See the GNU
* General Public License, version 3, for more details.
*
* A copy of the GNU General Public License, version 3, is available
* at http://www.r-project.org/Licenses/GPL-3
*
* C functions for the R/qtl package
*
* These functions are for performing a two-dimensional genome scan with
* a two-QTL model by Haley-Knott regression
*
* Contains: R_scantwo_1chr_binary_hk, scantwo_1chr_binary_hk,
* R_scantwo_2chr_binary_hk, scantwo_2chr_binary_hk
*
**********************************************************************/
/**********************************************************************
*
* R_scantwo_1chr_binary_hk
*
* Wrapper for call from R; reorganizes genotype prob and result matrix
* and calls scantwo_1chr_binary_hk.
*
**********************************************************************/
void R_scantwo_1chr_binary_hk(int *n_ind, int *n_pos, int *n_gen,
double *genoprob, double *pairprob,
double *addcov, int *n_addcov,
double *intcov, int *n_intcov,
double *pheno,
double *result, int *n_col2drop, int *col2drop,
double *tol, int *maxit, int *verbose);
/**********************************************************************
*
* scantwo_1chr_binary_hk
*
* Performs a 2-dimensional genome scan using the Haley-Knott
* regression method (regressing phenotypes on conditional genotype
* probabilities) for a two-QTL model with the two QTL residing on
* the same chromosome.
*
* 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]
*
* Pairprob Array of joint genotype probabilities for QTL
* pairs; indexed as Pairprob[gen1][gen2][pos1][pos2][ind]
* where pos2 > pos1 (for pos2 <= pos1, points to nothing)
*
* Addcov Matrix of additive covariates: Addcov[cov][ind]
*
* n_addcov Number of columns of Addcov
*
* Intcov Number of interactive covariates: Intcov[cov][ind]
*
* n_intcov Number of columns of Intcov
*
* pheno Phenotype data, as a vector
*
* Result vector to contain LOD scores
* triangle (row > col) contains the joint LODs while
* the upper triangle (row < col) contains the LODs for
* testing epistasis.
* Note: indexed as Result[col][row]
*
* n_col2drop For X chromosome, number of columns to drop
*
* col2drop For X chromosome, indicates which columns to drop
*
**********************************************************************/
void scantwo_1chr_binary_hk(int n_ind, int n_pos, int n_gen, double ***Genoprob,
double *****Pairprob, double **Addcov, int n_addcov,
double **Intcov, int n_intcov, double *pheno,
double **Result, int n_col2drop,
int *col2drop, double tol, int maxit, int verbose);
/**********************************************************************
*
* R_scantwo_2chr_binary_hk
*
* Wrapper for call from R; reorganizes genotype prob and result matrix
* and calls scantwo_2chr_binary_hk.
*
**********************************************************************/
void R_scantwo_2chr_binary_hk(int *n_ind, int *n_pos1, int *n_pos2,
int *n_gen1, int *n_gen2,
double *genoprob1, double *genoprob2,
double *addcov, int *n_addcov,
double *intcov, int *n_intcov,
double *pheno,
double *result_full, double *result_add,
double *tol, int *maxit, int *verbose);
/**********************************************************************
*
* scantwo_2chr_binary_hk
*
* Performs a 2-dimensional genome scan using the Haley-Knott
* regression method (regressing phenotypes on conditional genotype
* probabilities) for a two-QTL model with the two QTL residing on
* the different chromosomes.
*
* n_ind Number of individuals
*
* n_pos1 Number of marker positions on first chromosome
*
* n_pos2 Number of marker positions on second chromosome
*
* n_gen1 Number of different genotypes for first chromosome
*
* n_gen2 Number of different genotypes for second chromosome
*
* Genoprob1 Array of conditional genotype probs for 1st chr
* Indexed as Genoprob[gen][pos][ind]
*
* Genoprob2 Array of conditional genotype probs for 2nd chr
*
* Addcov Matrix of additive covariates: Addcov[cov][ind]
*
* n_addcov Number of columns of Addcov
*
* Intcov Number of interactive covariates: Intcov[cov][ind]
*
* n_intcov Number of columns of Intcov
*
* pheno Phenotype data, as a vector
*
* Result_full Result matrix of size [n_pos1 x n_pos2]
* containing the joint LODs
* Note: indexed as Result[pos1][pos2]
*
* Result_add Result matrix of size [n_pos2 x n_pos1]
* containing the LODs for add've models
* also indexed as Result[pos2][pos1]
*
**********************************************************************/
void scantwo_2chr_binary_hk(int n_ind, int n_pos1, int n_pos2, int n_gen1,
int n_gen2, double ***Genoprob1,
double ***Genoprob2,
double **Addcov, int n_addcov,
double **Intcov, int n_intcov, double *pheno,
double **Result_full, double **Result_add,
double tol, int maxit, int verbose);
/* end of scantwo_binary_hk.h */
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