update documentation

mmollina · Feb 13, 2024 · 4ece3ff · 4ece3ff
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Showing 7 changed files with 100 additions and 34 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -84,6 +84,8 @@ export(mf_k)
 export(mp_pallet1)
 export(mp_pallet2)
 export(mp_pallet3)
+export(paralell_pairwise_discrete)
+export(paralell_pairwise_probability)
 export(parallel_block)
 export(ph_list_to_matrix)
 export(ph_matrix_to_list)

diff --git a/R/make_seq.R b/R/make_seq.R
@@ -30,12 +30,12 @@
 #'
 #' @return Returns an object of class \code{mappoly.sequence}, comprising:
 #' \itemize{
-#'   \item{\code{seq.num}}{Ordered vector of marker indices according to the input.}
-#'   \item{\code{seq.phases}}{List of linkage phases between markers; \code{-1} for undefined phases.}
-#'   \item{\code{seq.rf}}{Vector of recombination frequencies; \code{-1} for unestimated frequencies.}
-#'   \item{\code{loglike}}{Log-likelihood of the linkage map.}
-#'   \item{\code{data.name}}{Name of the \code{mappoly.data} object with raw data.}
-#'   \item{\code{twopt}}{Name of the \code{mappoly.twopt} object with 2-point analyses; \code{-1} if not computed.}
+#'   \item{seq.num}{Ordered vector of marker indices according to the input.}
+#'   \item{seq.phases}{List of linkage phases between markers; \code{-1} for undefined phases.}
+#'   \item{seq.rf}{Vector of recombination frequencies; \code{-1} for not estimated frequencies.}
+#'   \item{loglike}{Log-likelihood of the linkage map.}
+#'   \item{data.name}{Name of the \code{mappoly.data} object with raw data.}
+#'   \item{twopt}{Name of the \code{mappoly.twopt} object with 2-point analyses; \code{-1} if not computed.}
 #' }
 #'
 #' @examples

diff --git a/R/pairwise_rf.R b/R/pairwise_rf.R
@@ -249,8 +249,20 @@ est_pairwise_rf <- function(input.seq, count.cache = NULL,
                    class = "mappoly.twopt"))
 }
 
-#' Wrapper function to discrete-based pairwise two-point estimation in C++
+#' Parallel Pairwise Discrete Estimation
+#'
+#' This function performs parallel pairwise estimation of recombination fractions using discrete dosage scoring via a C++ backend.
+#' @param mrk.pairs A matrix of dimensions 2*N, containing N pairs of markers to be analyzed.
+#' @param input.seq An object of class \code{mappoly.sequence}.
+#' @param geno Genotype matrix.
+#' @param dP Vector of probabilities for the first allele.
+#' @param dQ Vector of probabilities for the second allele.
+#' @param count.cache An object of class \code{cache.info} containing pre-computed genotype frequencies.
+#' @param tol The tolerance level for the estimation accuracy (default is \code{.Machine$double.eps^0.25}).
+#' @param ll Logical; if TRUE, the function returns log-likelihood values instead of LOD scores. For internal use.
+#' @return Depending on the \code{ll} parameter, returns either log-likelihood values or formatted LOD scores from pairwise recombination fraction estimation.
 #' @keywords internal
+#' @export
 paralell_pairwise_discrete <- function(mrk.pairs,
                                        input.seq,
                                        geno,
@@ -273,8 +285,20 @@ paralell_pairwise_discrete <- function(mrk.pairs,
   return(lapply(res, format_rf))
 }
 
-#' Wrapper function to probability-based pairwise two-point estimation in C++
+#' Parallel Pairwise Probability Estimation
+#'
+#' This function performs parallel pairwise estimation of recombination fractions using probability-based dosage scoring via a C++ backend.
+#' @param mrk.pairs A matrix of dimensions 2*N, containing N pairs of markers to be analyzed.
+#' @param input.seq An object of class \code{mappoly.sequence}.
+#' @param geno Genotype matrix.
+#' @param dP Vector of probabilities for the first allele.
+#' @param dQ Vector of probabilities for the second allele.
+#' @param count.cache An object of class \code{cache.info} containing pre-computed genotype frequencies.
+#' @param tol The tolerance level for the estimation accuracy (default is \code{.Machine$double.eps^0.25}).
+#' @param ll Logical; if TRUE, the function returns log-likelihood values instead of LOD scores. For internal use.
+#' @return Depending on the \code{ll} parameter, returns either log-likelihood values or formatted LOD scores from pairwise recombination fraction estimation.
 #' @keywords internal
+#' @export
 paralell_pairwise_probability <- function(mrk.pairs,
                                           input.seq,
                                           geno,

diff --git a/man/make_seq_mappoly.Rd b/man/make_seq_mappoly.Rd
diff --git a/man/paralell_pairwise_discrete.Rd b/man/paralell_pairwise_discrete.Rd
diff --git a/man/paralell_pairwise_probability.Rd b/man/paralell_pairwise_probability.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -59,22 +59,22 @@ BEGIN_RCPP
 END_RCPP
 }
 
-RcppExport SEXP calc_genoprob(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP calc_genoprob_prior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP calc_genprob_haplo(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP calc_genprob_haplo_highprec(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP calc_genprob_single_parent(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP est_haplotype_map(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP est_haplotype_map_highprec(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP est_hmm_map_single_parent(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP est_map_hmm(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP est_map_hmm_highprec(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP get_counts_single_parent_cpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP loglike_hmm(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP pairwise_rf_estimation_disc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP pairwise_rf_estimation_disc_rcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP pairwise_rf_estimation_prob(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-RcppExport SEXP poly_hmm_est_CPP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP calc_genoprob(void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP calc_genoprob_prior(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP calc_genprob_haplo(void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP calc_genprob_haplo_highprec(void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP calc_genprob_single_parent(void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP est_haplotype_map(void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP est_haplotype_map_highprec(void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP est_hmm_map_single_parent(void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP est_map_hmm(void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP est_map_hmm_highprec(void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP get_counts_single_parent_cpp(void *, void *, void *, void *, void *, void *);
+RcppExport SEXP loglike_hmm(void *, void *, void *, void *, void *, void *);
+RcppExport SEXP pairwise_rf_estimation_disc(void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP pairwise_rf_estimation_disc_rcpp(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP pairwise_rf_estimation_prob(void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP poly_hmm_est_CPP(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_mappoly_vcf_get_probabilities", (DL_FUNC) &_mappoly_vcf_get_probabilities, 2},