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License: MIT License
Genetic Linkage Maps in Autopolyploids v 2.0
License: MIT License
I constructed a map using BExMG and SWxBE and trying to integrate the two... in the calc_consensus_haplo() if i set ncpus=2 then it says, "Error in get(name, envir = envir) : object 'pedigree' not found"
ncpus=1 works fine.
thanks
Jeekin
Hi @mmollina
Since I prefer to organise complex workflows like mapping in targets pipelines, I am interested to discuss what would be the best ways to work with mappoly2 objects and workflows.
It was very difficult to do this in mappoly due to references to external objects.
#> Multi-locus map estimation
s <- mapping(s, type = "mds", parent = "p1", ncpus = ncores)
s <- mapping(s, type = "genome", parent = "p1", ncpus = ncores)
s <- mapping(s, type = "mds", parent = "p2", ncpus = ncores)
s <- mapping(s, type = "genome", parent = "p2", ncpus = ncores)
Using vignette data or my own raises the following:
> ## testing plot_map
> download.file("https://github.com/mmollina/mappoly2_vignettes/raw/main/I195_x_F1-85-209_map.rda",
+ destfile = "temp_file.rda")
trying URL 'https://github.com/mmollina/mappoly2_vignettes/raw/main/I195_x_F1-85-209_map.rda'
Content type 'application/octet-stream' length 11822960 bytes (11.3 MB)
==================================================
downloaded 11.3 MB
> load("temp_file.rda")
> ## testing plot_map
> library(mappoly2)
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
> load("temp_file.rda")
> ls()
[1] "I195xF1_85_209_map"
> # just build first lg
> I195xF1_85_209_map <- mapping(I195xF1_85_209_map,
+ lg = 1,
+ type = "genome",
+ error = 0.05, ncpus = 4)
Multi-locus map estimation
Processing linkage group
Conf. 1 :..............................
..............................
................
Done with map estimation
> plot_map(I195xF1_85_209_map,type = 'genome')
Error: assert_that: missing values present in assertion
Dear Mollinari,
Thanks for your developing excellent software in polyploid genetics. I'm trying to build a genetic map of sweet potato using mappoly2 latest, and after using rf_filter(px.f1.all, thresh.LOD.ph = 5, thresh.LOD.rf = 5, thresh.rf = 0.15, probs = c(0.05, 0.9))
, then running group(x = px.f1.all, expected.groups = 5, comp.mat = TRUE, inter = TRUE, LODweight = TRUE)"
, returns "Error in hclust(as.dist(MSNP), method = "ward.D2", members = apply(Mlod, : invalid length of members", is this an unknown bug and is there any suggestion to solve it?
Bestly,
Jun Zhang
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