vignettes/import_from_qtl.md

In StefanReuscher/ABHgenotypeR: Easy Visualization of ABH Genotypes

Import maps from 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.

Import maps from 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" , ...)

StefanReuscher/ABHgenotypeR documentation built on May 9, 2019, 3:05 p.m.