From f5960f59d30a2ee9a2f49d2b9c6cfc9d1dcf4450 Mon Sep 17 00:00:00 2001 From: Marcelo Mollinari Date: Fri, 20 Oct 2023 06:46:40 -0400 Subject: [PATCH] Update split_and_rephase.R --- R/split_and_rephase.R | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/R/split_and_rephase.R b/R/split_and_rephase.R index 0d4b1488..a8a8837f 100644 --- a/R/split_and_rephase.R +++ b/R/split_and_rephase.R @@ -20,6 +20,8 @@ #' #' @param phase.config which phase configuration should be used. "best" (default) #' will choose the maximum likelihood phase configuration +#' +#' @param tol.merge the desired accuracy for merging maps (default = 10e-04) #' #' @param tol.final the desired accuracy for the final map (default = 10e-04) #' @@ -51,6 +53,7 @@ split_and_rephase <- function(input.map, gap.threshold = 5, size.rem.cluster = 1, phase.config = "best", + tol.merge = 10e-4, tol.final = 10e-4, verbose = TRUE){ if (!inherits(input.map, "mappoly.map")) { @@ -119,10 +122,11 @@ split_and_rephase <- function(input.map, verbose = FALSE) } else { - newmap <- merge_maps(list(newmap, temp.maps[[i]]), + newmap <- merge_maps(map.list = list(newmap, temp.maps[[i]]), twopt = twopt, thres.twopt = 10, - thres.hmm = 50) + thres.hmm = 50, + tol = tol.merge) } newmap <- filter_map_at_hmm_thres(newmap, thres.hmm = 0.01) }