From 0614559901855f4d3697d1ae539db53740c62a74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cgabrielgesteira=E2=80=9D?= <“gabrielgesteira@gmail.com”> Date: Sun, 3 Sep 2023 20:15:45 -0400 Subject: [PATCH 1/5] Improving calc_homologprob - Matrix-based calculations for homolog probabilities - Runs 2x faster than previous version --- R/homolog_probs.R | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/R/homolog_probs.R b/R/homolog_probs.R index e3e89f08..ebea7f9c 100644 --- a/R/homolog_probs.R +++ b/R/homolog_probs.R @@ -55,8 +55,23 @@ calc_homologprob <- function(input.genoprobs, verbose = TRUE){ ploidy <- v[as.character(length(stt.names))] hom.prob <- array(NA, dim = c(ploidy*2, length(mrk.names), length(ind.names))) dimnames(hom.prob) <- list(letters[1:(2*ploidy)], mrk.names, ind.names) - for(i in letters[1:(2*ploidy)]) - hom.prob[i,,] <- apply(input.genoprobs[[j]]$probs[grep(stt.names, pattern = i),,], c(2,3), function(x) round(sum(x, na.rm = TRUE),4)) + ## for(i in letters[1:(2*ploidy)]) + ## hom.prob[i,,] <- apply(input.genoprobs[[j]]$probs[grep(stt.names, pattern = i),,], c(2,3), function(x) round(sum(x, na.rm = TRUE),4)) + ## Incidence matrix for homologs + alleles = matrix(unlist(strsplit(stt.names, '')), ncol=(ploidy+1), byrow=TRUE)[,-c((ploidy/2)+1)] + ## Creating incidence matrix to transition from genotypes to homologs + alleles2 = matrix(0, length(stt.names), ploidy*2) + ## Creating dummy variables to associate genotypes with alleles + for(i in 1:nrow(alleles)){ + for(k in 1:ncol(alleles)){ + alleles2[i,match(alleles[i,k], letters)]=1.000000 + } + } + ## Getting homolog probabilities + for(m in 1:length(mrk.names)) { + hom.prob[,m,] <- round(t(alleles2)%*%input.genoprobs[[j]]$probs[,m,],4) + ## hom.prob[,m,] <- round(t(alleles2)%*%input.genoprobs[[j]]$probs[,m,], 4) + } df.hom <- reshape2::melt(hom.prob) map <- data.frame(map.position = input.genoprobs[[j]]$map, marker = names(input.genoprobs[[j]]$map)) colnames(df.hom) <- c("homolog", "marker", "individual", "probability") From 13f33c518fa5dd46927287aaa0a68c2639eb9ef8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cgabrielgesteira=E2=80=9D?= <“gabrielgesteira@gmail.com”> Date: Sun, 3 Sep 2023 20:19:06 -0400 Subject: [PATCH 2/5] Small change to long dummy variable --- R/homolog_probs.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/homolog_probs.R b/R/homolog_probs.R index ebea7f9c..cd264381 100644 --- a/R/homolog_probs.R +++ b/R/homolog_probs.R @@ -64,7 +64,7 @@ calc_homologprob <- function(input.genoprobs, verbose = TRUE){ ## Creating dummy variables to associate genotypes with alleles for(i in 1:nrow(alleles)){ for(k in 1:ncol(alleles)){ - alleles2[i,match(alleles[i,k], letters)]=1.000000 + alleles2[i,match(alleles[i,k], letters)]=1.00 } } ## Getting homolog probabilities From 116bab6a782b4272be484712a5ef15e6108ae7a2 Mon Sep 17 00:00:00 2001 From: Jeekin Lau Date: Thu, 9 Nov 2023 21:17:17 -0600 Subject: [PATCH 3/5] Update plot_progeny_dosage_change.R add in argument to output an imputed and corrected dosage matrix. --- R/plot_progeny_dosage_change.R | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R index 24b21910..fcefeb5e 100644 --- a/R/plot_progeny_dosage_change.R +++ b/R/plot_progeny_dosage_change.R @@ -11,13 +11,14 @@ #' #' @param error error rate used in global error in the `calc_genoprob_error()` #' @param verbose T or F for `calc_genoprob_error()` and `calc_homologprob()` -#' +#' @param output_corrected TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output. #' #' @return A ggplot of the changed and imputed genotypic dosages #' #' @examples -#' x<-get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) -#' plot_progeny_dosage_change(list(x), error=0.05) +#' x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) # subset to run fast in tests +#' plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) # no new corrected dosages +#' corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected #' #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu} #' @@ -25,7 +26,7 @@ #' @import reshape2 #' @export plot_progeny_dosage_change -plot_progeny_dosage_change <- function(map_list, error, verbose=T){ +plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_corrected=F){ Var1 <- Var2 <- value <- NULL map=map_list if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here") @@ -175,8 +176,17 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){ guides(fill=guide_legend(title="Dosage change")) print("done") - return(plot1) - + print(plot1) + if (output_corrected ==T){ + mrk_names=rownames(finished) + mrk_index=which(dat$mrk.names%in%mrk_names) + P1 = dat$dosage.p1[mrk_index] + P2 = dat$dosage.p2[mrk_index] + sequence = dat$chrom[mrk_index] + sequence_position = dat$genome.pos[mrk_index] + + hmm_imputed = cbind(P1,P2,sequence,sequence_position, finished) + return(hmm_imputed)} } From b7f8890993c0b135ce3652ca8290e290dfefa27c Mon Sep 17 00:00:00 2001 From: Jeekin Lau Date: Thu, 9 Nov 2023 21:20:18 -0600 Subject: [PATCH 4/5] update documentation --- man/plot_progeny_dosage_change.Rd | 9 ++++++--- man/split_and_rephase.Rd | 15 +++++++++++++++ src/RcppExports.cpp | 32 +++++++++++++++---------------- 3 files changed, 37 insertions(+), 19 deletions(-) diff --git a/man/plot_progeny_dosage_change.Rd b/man/plot_progeny_dosage_change.Rd index 03666482..710b8d0f 100644 --- a/man/plot_progeny_dosage_change.Rd +++ b/man/plot_progeny_dosage_change.Rd @@ -4,7 +4,7 @@ \alias{plot_progeny_dosage_change} \title{Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error} \usage{ -plot_progeny_dosage_change(map_list, error, verbose = T) +plot_progeny_dosage_change(map_list, error, verbose = T, output_corrected = F) } \arguments{ \item{map_list}{a list of multiple \code{mappoly.map.list}} @@ -12,6 +12,8 @@ plot_progeny_dosage_change(map_list, error, verbose = T) \item{error}{error rate used in global error in the `calc_genoprob_error()`} \item{verbose}{T or F for `calc_genoprob_error()` and `calc_homologprob()`} + +\item{output_corrected}{TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output.} } \value{ A ggplot of the changed and imputed genotypic dosages @@ -25,8 +27,9 @@ Most recent update 8/29/2023: -un-hardcoded linkage groups in maps. previously hard-coded for tetraploid rose. } \examples{ - x<-get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) - plot_progeny_dosage_change(list(x), error=0.05) + x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) # subset to run fast in tests + plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) # no new corrected dosages + corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected } \author{ diff --git a/man/split_and_rephase.Rd b/man/split_and_rephase.Rd index d45e6731..e97fd16a 100644 --- a/man/split_and_rephase.Rd +++ b/man/split_and_rephase.Rd @@ -10,6 +10,9 @@ split_and_rephase( gap.threshold = 5, size.rem.cluster = 1, phase.config = "best", + thres.twopt = 3, + thres.hmm = "best", + tol.merge = 0.001, tol.final = 0.001, verbose = TRUE ) @@ -32,6 +35,18 @@ value is 1} \item{phase.config}{which phase configuration should be used. "best" (default) will choose the maximum likelihood phase configuration} +\item{thres.twopt}{the threshold used to determine if the linkage +phases compared via two-point analysis should be considered +for the search space reduction (default = 3)} + +\item{thres.hmm}{the threshold used to determine which linkage +phase configurations should be returned when merging two maps. +If "best" (default), returns only the best linkage phase +configuration. NOTE: if merging multiple maps, it always uses +the "best" linkage phase configuration at each block insertion.} + +\item{tol.merge}{the desired accuracy for merging maps (default = 10e-04)} + \item{tol.final}{the desired accuracy for the final map (default = 10e-04)} \item{verbose}{if \code{TRUE} (default), the current progress is shown; if diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 7e21fe7e..bf307dcc 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -59,22 +59,22 @@ BEGIN_RCPP END_RCPP } -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 *, 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 *); +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, 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); static const R_CallMethodDef CallEntries[] = { {"_mappoly_vcf_get_probabilities", (DL_FUNC) &_mappoly_vcf_get_probabilities, 2}, From 637c5a105fc579882961854b2108667be00cccc5 Mon Sep 17 00:00:00 2001 From: Marcelo Mollinari Date: Fri, 24 Nov 2023 12:37:32 -0500 Subject: [PATCH 5/5] Updating documentation and eliminating C++11 requirement --- DESCRIPTION | 2 +- R/plot_progeny_dosage_change.R | 41 +++++++++++++++++-------------- man/plot_progeny_dosage_change.Rd | 30 ++++++++++++---------- src/Makevars.win | 2 -- src/RcppExports.cpp | 32 ++++++++++++------------ 5 files changed, 56 insertions(+), 51 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 09473eb3..de9070cf 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -90,7 +90,7 @@ Imports: plotly LinkingTo: Rcpp, RcppParallel RoxygenNote: 7.2.3 -SystemRequirements: C++11, GNU make +SystemRequirements: GNU make Encoding: UTF-8 Suggests: testthat, diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R index fcefeb5e..17b22e74 100644 --- a/R/plot_progeny_dosage_change.R +++ b/R/plot_progeny_dosage_change.R @@ -1,32 +1,34 @@ -#' Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error +#' Display genotypes imputed or changed by the HMM chain given a global genotypic error #' #' Outputs a graphical representation ggplot with the percent of data changed. -#' -#' Most recent update 8/29/2023: -#' -fixed issue where only worked on tetraploid to now working for diploid to octaploid. -#' -un-hardcoded linkage groups in maps. previously hard-coded for tetraploid rose. -#' #' #' @param map_list a list of multiple \code{mappoly.map.list} #' #' @param error error rate used in global error in the `calc_genoprob_error()` -#' @param verbose T or F for `calc_genoprob_error()` and `calc_homologprob()` -#' @param output_corrected TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output. +#' @param verbose if TRUE (default), current progress is shown; if FALSE, +#' no output is produced +#' @param output_corrected logical. if FALSE only the ggplot of the changed +#' dosage is printed, if TRUE then a new corrected dosage matrix is output. #' #' @return A ggplot of the changed and imputed genotypic dosages #' #' @examples -#' x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) # subset to run fast in tests -#' plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) # no new corrected dosages -#' corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected +#' x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) +#' plot_progeny_dosage_change(list(x), error=0.05, output_corrected=FALSE) +#' corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, +#' output_corrected=FALSE) #output corrected #' -#' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu} +#' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane +#' Taniguti, \email{chtaniguti@tamu.edu} #' #' @import ggplot2 #' @import reshape2 #' @export plot_progeny_dosage_change -plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_corrected=F){ +plot_progeny_dosage_change <- function(map_list, + error, + verbose = TRUE, + output_corrected = FALSE){ Var1 <- Var2 <- value <- NULL map=map_list if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here") @@ -38,7 +40,8 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc genoprob <- vector("list", length(map)) for(i in 1:length(map)){ - genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, verbose = verbose) + genoprob[[i]] <- calc_genoprob_error(input.map = map[[i]], error = error, + verbose = verbose) } print("calculating homologprob") @@ -47,8 +50,8 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc print("comparing to orginal") - P=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$P), recursive=F) - Q=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$Q), recursive=F) + P=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$P), recursive=FALSE) + Q=unlist(lapply(map, function(x) x$maps[[1]]$seq.ph$Q), recursive=FALSE) @@ -92,7 +95,7 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc test <- sapply(homoprob_ind, function(x) { by_marker <- split.data.frame(x, x[,1]) - final_matrix <- t(sapply(by_marker, function(y) y[order(y[,4], decreasing = T),][1:ploidy,2])) + final_matrix <- t(sapply(by_marker, function(y) y[order(y[,4], decreasing = TRUE),][1:ploidy,2])) final_vector <- apply(final_matrix, 1, function(w) paste0(w, collapse = "")) return(final_vector) }) @@ -169,7 +172,7 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc empty_matrix[which(!original_geno==finished&!original_geno==ploidy+1)]="changed" empty_matrix_melt=melt(empty_matrix) plot1<-ggplot(empty_matrix_melt, aes(Var1, Var2, fill= factor(value, levels=c("changed","imputed","unchanged")))) + - geom_tile()+scale_fill_manual(values=colors, drop=F)+ + geom_tile()+scale_fill_manual(values=colors, drop=FALSE)+ xlab("Markers")+ ylab("Individuals")+ ggtitle(paste0("changed = ",round(percent_changed, digits=3),"% ","imputed = ", round(percent_imputed, digits=3),"%"))+ @@ -177,7 +180,7 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_correc print("done") print(plot1) - if (output_corrected ==T){ + if (output_corrected ==TRUE){ mrk_names=rownames(finished) mrk_index=which(dat$mrk.names%in%mrk_names) P1 = dat$dosage.p1[mrk_index] diff --git a/man/plot_progeny_dosage_change.Rd b/man/plot_progeny_dosage_change.Rd index 710b8d0f..6fa79942 100644 --- a/man/plot_progeny_dosage_change.Rd +++ b/man/plot_progeny_dosage_change.Rd @@ -2,18 +2,25 @@ % Please edit documentation in R/plot_progeny_dosage_change.R \name{plot_progeny_dosage_change} \alias{plot_progeny_dosage_change} -\title{Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error} +\title{Display genotypes imputed or changed by the HMM chain given a global genotypic error} \usage{ -plot_progeny_dosage_change(map_list, error, verbose = T, output_corrected = F) +plot_progeny_dosage_change( + map_list, + error, + verbose = TRUE, + output_corrected = FALSE +) } \arguments{ \item{map_list}{a list of multiple \code{mappoly.map.list}} \item{error}{error rate used in global error in the `calc_genoprob_error()`} -\item{verbose}{T or F for `calc_genoprob_error()` and `calc_homologprob()`} +\item{verbose}{if TRUE (default), current progress is shown; if FALSE, +no output is produced} -\item{output_corrected}{TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output.} +\item{output_corrected}{logical. if FALSE only the ggplot of the changed +dosage is printed, if TRUE then a new corrected dosage matrix is output.} } \value{ A ggplot of the changed and imputed genotypic dosages @@ -21,17 +28,14 @@ A ggplot of the changed and imputed genotypic dosages \description{ Outputs a graphical representation ggplot with the percent of data changed. } -\details{ -Most recent update 8/29/2023: - -fixed issue where only worked on tetraploid to now working for diploid to octaploid. - -un-hardcoded linkage groups in maps. previously hard-coded for tetraploid rose. -} \examples{ - x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) # subset to run fast in tests - plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) # no new corrected dosages - corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected + x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE) + plot_progeny_dosage_change(list(x), error=0.05, output_corrected=FALSE) + corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, + output_corrected=FALSE) #output corrected } \author{ -Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu} +Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane +Taniguti, \email{chtaniguti@tamu.edu} } diff --git a/src/Makevars.win b/src/Makevars.win index 09d564ce..8503f143 100644 --- a/src/Makevars.win +++ b/src/Makevars.win @@ -1,7 +1,5 @@ PKG_LIBS = -lz -CXX_STD = CXX11 - PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=1 PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" \ diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index bf307dcc..7e21fe7e 100644 --- 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, 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 *, 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},