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3_analyse_map_quality.Rmd

This file is part of "Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population".

Version 1.0
File Citation
Brault, Charlotte; Flutre, Timothée; Launay, Amandine; Doligez, Agnès; Chouiki, Hajar; Sarah, Gautier; Mournet, Pierre, 2021, "3_analyse_map_quality.Rmd", Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population, https://doi.org/10.15454/QEDX2V/ZGU8W5, Portail Data INRAE, V1
Dataset Citation
Brault, Charlotte; Flutre, Timothée; Launay, Amandine; Doligez, Agnès; Chouiki, Hajar; Sarah, Gautier; Mournet, Pierre, 2021, "Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population", https://doi.org/10.15454/QEDX2V, Portail Data INRAE, V1, UNF:6:L5hd7gugVIod43JkBypJvQ== [fileUNF]
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doi:10.15454/QEDX2V/ZGU8W5
71b7bf1c5a1beb551eee9fd660bef041
2021-05-25
8.7 KB
text/x-r-markdown
R script that we used to produce different statistical tests and diagnostic plots to check map quality. It takes as input the 3 files created with "2_create_genetic_map_lepmap_SxG.Rmd" ("SxG_GBS_lepmap.loc", "SxG_GBS_lepmap.map", "SxG_GBS.qua"). Map quality was analyzed with R/qtl functions (Broman et al. 2003): droponemarker for dropping one marker at a time and rf for plotting two-point recombination fractions and LOD scores. Genotyping error rate was also estimated. We had to remove three outlier markers by hand because they were on the Unknown chromosome. The resulting map had 3,961 fully-informative markers (abxcd segregation) without missing data. This script produces 2 output files: "SxG_GBS.loc" and "SxG_GBS_lepmap_v2.map" (which also need to be modified by hand in order to generate "SxG_GBS.map").
2020-10-15
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