qtl
or ASMap
packages into ABHgenotypeR
The python script https://github.com/MichelMoser/GBS2map.git (M. Moser) converts ASMap
or qtl
cross objects to a format ABHgenotypeR
can import. An error is produced if the given map contains a linkage group containing a single marker only.
write.cross(your_map, format="csv", filestem = "name_of_your_map")
In a Terminal:
python3 Rqtl_2_abh.py name_of_your_map.csv name_of_abh_compatible_map.csv
To read in the produced file with ABHgenotypeR
:
map <- readABHgenotypes("name_of_abh_compatible_map.csv")
The file is ready for use in ABHgenotypeR
now.
ABHgenotypeR
to qtl
or ASMap
writeABHgenotypes(map, outfile = "name_of_your_map.csv")
If the file can not be directly read in to qtl
/ASMap
, it needs two small changes: The first value in the first row needs to be changed from "id" to "Genotype" and the second value in the same column needs to be changed from "NA" to "".
| id | marker1 | marker2 | ... | |----- |----- |----- |----- | | NA | 1 | 1 | ... | | ind1 | B | A | ... | | ind2 | B | B | ... | | ... | ... | ... | ... |
| Genotype | marker1 | marker2 | ... | |----- |----- |----- |----- | | | 1 | 1 | ... | | ind1 | B | A | ... | | ind2 | B | B | ... | | ... | ... | ... | ... |
The file can now be read in with
map <- read.cross(format = "csv", file = "name_of_your_map.csv" , ...)
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