From b7f8890993c0b135ce3652ca8290e290dfefa27c Mon Sep 17 00:00:00 2001 From: Jeekin Lau Date: Thu, 9 Nov 2023 21:20:18 -0600 Subject: [PATCH] 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},