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R/est_map_hmm.R
changed.
@@ -514,7 +514,7 @@
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| 514 | 514 | seq.num <- tail.temp$maps[[i]]$seq.num |
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| 515 | 515 | if(length(seq.num) < extend.tail) |
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| 516 | 516 | seq.num <- tail(cur.map$maps[[i]]$seq.num, extend.tail) |
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| 517 | - | ## If the tail do not contain the marker responsable for carrying |
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| 517 | + | ## If the tail do not contain the marker responsible for carrying |
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| 518 | 518 | ## multiple linkage phases through the rounds of insertion, |
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| 519 | 519 | ## extend the tail so it contains that marker |
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| 520 | 520 | if(max(check_ls_phase(all.ph)) >= length(seq.num)){ |
@@ -537,15 +537,15 @@
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| 537 | 537 | ## information obtained in the current round |
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| 538 | 538 | twopt.phase.number<-length(input.ph$config.to.test) |
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| 539 | 539 | ## If this number is higher than phase.number.limit, |
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| 540 | - | ## procede to the next iteration |
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| 540 | + | ## proceed to the next iteration |
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| 541 | 541 | if(length(input.ph$config.to.test) > phase.number.limit) { |
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| 542 | 542 | if(verbose) |
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| 543 | 543 | cat(crayon::italic$yellow(paste0(ct ,": not included (linkage phases)\n", sep = ""))) |
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| 544 | 544 | ct <- ct + 1 |
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| 545 | 545 | next() |
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| 546 | 546 | } |
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| 547 | 547 | ## Appending the marker to the numeric |
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| 548 | - | ## sequence and makeing a new sequence |
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| 548 | + | ## sequence and making a new sequence |
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| 549 | 549 | seq.num <- c(seq.num, input.seq$seq.num[ct]) |
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| 550 | 550 | seq.cur <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos=1), |
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| 551 | 551 | arg = seq.num, |
@@ -613,12 +613,14 @@
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| 613 | 613 | } else { selected.map <- LOD < thres.hmm } |
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| 614 | 614 | all.ph.temp <- update_ph_list_at_hmm_thres(cur.map.temp, Inf) |
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| 615 | 615 | cur.map.temp$maps <- cur.map.temp$maps[selected.map] |
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| 616 | + | id <- !sapply(cur.map.temp$maps, is.null) |
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| 617 | + | cur.map.temp$maps <- cur.map.temp$maps[id] |
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| 616 | 618 | cur.map <- cur.map.temp |
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| 617 | - | all.ph <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[selected.map,,drop=FALSE]) |
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| 619 | + | all.ph <- add_mrk_at_tail_ph_list(all.ph, all.ph.temp, M[id,,drop=FALSE]) |
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| 618 | 620 | ct <- ct + 1 |
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| 619 | 621 | } |
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| 620 | - | ##### Reestimating final map #### |
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| 621 | - | ## Reestimating final map with higher tolerance |
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| 622 | + | ##### Re-estimating final map #### |
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| 623 | + | ## Re-estimating final map with higher tolerance |
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| 622 | 624 | seq.final <- make_seq_mappoly(input.obj = get(input.seq$data.name, pos=1), |
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| 623 | 625 | arg = as.numeric(names(all.ph$config.to.test[[1]]$P)), |
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| 624 | 626 | data.name = input.seq$data.name) |
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