Nothing
## ----load_cache,echo=FALSE-----------------------------------------------
# To speed up vignette building, we load some cached results here
load(system.file("example/cached.results.RData",package = "BatchMap"))
## ----reading_data, eval=TRUE---------------------------------------------
suppressPackageStartupMessages(library(BatchMap))
input_file <- system.file("example/sim7.5k.txt.gz",package = "BatchMap")
outcross <- read.outcross2(input_file)
outcross
## ----resolve_bins, eval=TRUE---------------------------------------------
bins <- find.bins(outcross, exact = FALSE)
outcross_clean <- create.data.bins(outcross, bins)
outcross_clean
## ----twopoints, eval=TRUE------------------------------------------------
twopt_table <- rf.2pts(outcross_clean)
# Check the size
format(object.size(twopt_table),units = "Mb")
## ----group, eval=TRUE----------------------------------------------------
linkage_groups <- group(make.seq(input.obj = twopt_table, "all"),
LOD = 12)
## ----split, eval=TRUE----------------------------------------------------
testcrosses <- pseudo.testcross.split(linkage_groups)
testcrosses$LG1.d2.15
## ----record, eval=FALSE--------------------------------------------------
# # The result of this function is cached
# ordered_sequences <- lapply(testcrosses, record.parallel, times = 10, cores = 1)
## ----pick_bs, eval=TRUE--------------------------------------------------
LG1_d1.10 <- ordered_sequences$LG1.d1.10
LG1_d2.15 <- ordered_sequences$LG1.d2.15
batch_size_LG1_d1.10 <- pick.batch.sizes(LG1_d1.10,
size = 50,
overlap = 30,
around = 10)
batch_size_LG1_d2.15 <- pick.batch.sizes(LG1_d2.15,
size = 50,
overlap = 30,
around = 10)
c(batch_size_LG1_d1.10, batch_size_LG1_d2.15)
## ----map_batches, eval=FALSE---------------------------------------------
# # The result of this function is cached
# map_LG1_d1.10 <- map.overlapping.batches(input.seq = LG1_d1.10,
# size = batch_size_LG1_d1.10,
# phase.cores = 4,
# overlap = 30)
## ---- print_maps, eval=TRUE----------------------------------------------
map_LG1_d1.10$Map
## ----ripple,eval=FALSE---------------------------------------------------
# # The result of this function is cached
# rip_LG1_d1.10 <- map.overlapping.batches(input.seq = LG1_d1.10,
# size = batch_size_LG1_d1.10,
# phase.cores = 4,
# overlap = 30,
# fun.order = ripple.ord,
# ripple.cores = 10,
# method = "one",
# min.tries = 1,
# ws = 4)
## ---- mistakes, eval=TRUE------------------------------------------------
err_rate <- function(seq)
{
# Get the marker position
s_num <- seq$seq.num
# If the sequence is reverse, turn it around
if(cor(s_num, 1:length(s_num)) < 0)
s_num <- rev(s_num)
# Get the number of misorders and divide by the total length
sum(order(s_num) - 1:length(s_num) != 0) / length(s_num)
}
c("BatchMap" = err_rate(map_LG1_d1.10$Map),
"RippleBatchMap" = err_rate(rip_LG1_d1.10$Map))
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