From 1273ce158ff7b178b46259f915288adea6abb2b9 Mon Sep 17 00:00:00 2001 From: Marcelo Mollinari Date: Fri, 20 Oct 2023 07:39:53 -0400 Subject: [PATCH] Update split_and_rephase.R --- R/split_and_rephase.R | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/R/split_and_rephase.R b/R/split_and_rephase.R index a8a8837f..3647e861 100644 --- a/R/split_and_rephase.R +++ b/R/split_and_rephase.R @@ -19,7 +19,17 @@ #' value is 1 #' #' @param phase.config which phase configuration should be used. "best" (default) -#' will choose the maximum likelihood phase configuration +#' will choose the maximum likelihood phase configuration + +#' @param 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) +#' +#' @param 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. #' #' @param tol.merge the desired accuracy for merging maps (default = 10e-04) #' @@ -53,6 +63,8 @@ split_and_rephase <- function(input.map, gap.threshold = 5, size.rem.cluster = 1, phase.config = "best", + thres.twopt = 3, + thres.hmm = "best", tol.merge = 10e-4, tol.final = 10e-4, verbose = TRUE){ @@ -124,8 +136,8 @@ split_and_rephase <- function(input.map, else { newmap <- merge_maps(map.list = list(newmap, temp.maps[[i]]), twopt = twopt, - thres.twopt = 10, - thres.hmm = 50, + thres.twopt = thres.twopt, + thres.hmm = thres.hmm, tol = tol.merge) } newmap <- filter_map_at_hmm_thres(newmap, thres.hmm = 0.01)