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text/tab-separated-values - 5.2 MB - MD5: 45840b16f6e101323853780f82ba48f7
The first column contains the sample identification number, and the other columns contain the absorbance data recorded from 802-2502 nm
text/tab-separated-values - 67.6 KB - MD5: 5a104479704927a627a186efcb3cd717
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text/tab-separated-values - 2.5 KB - MD5: 7d15599863e20712696e6a132a8a1ece
This table contains information about the BLUPs extraction process combined in "gather_BLUP_info.Rmd". For each trait, the following information is reported: “missing.data.percent”, percentage of missing values. “transformation”: transformation applied when raw data deviated fro...
text/x-r-markdown - 9.9 KB - MD5: 6ec5d16f6216055c18ca43a139dafdc9
This script creates simulated phenotypic values for two traits for the Syrah x Grenache progeny. It takes as input `SxG.allelic-effects.txt` with additive and dominance allelic effects with 3,961 SNP markers divided in allelic effects. It simulates multivariate phenotypic data (B...
text/x-r-markdown - 32.1 KB - MD5: 1b16d9f9aa133a97200e37f0f8b32038
R and bash script that we used to produce the Syrah x Grenache consensus genetic map with Lep-MAP3 (Rastas et al., 2017), from the SNP data filtered by grouping with Carthagene. It takes as inputs the cleaned vcf file and the pedigree file produced with «create_files_for_lepmap.R...
text/x-r-markdown - 8.7 KB - MD5: 71b7bf1c5a1beb551eee9fd660bef041
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...
application/x-shellscript - 1.1 KB - MD5: 915b0091de32de1a372f4b5d33382479
Bash script used for submitting the job on the SGE cluster with "OrderMarkers2" function from Lep-MAP3, during the "2_create_genetic_map_lepmap.Rmd" script. It performed the first ordering of markers, computed for each chromosome separately and repeated 5 times. Markers which wer...
application/x-shellscript - 1.1 KB - MD5: b1886cbffccec7bcc9990d773415dc83
Bash script used for submitting the job on the SGE cluster with "OrderMarkers2" function from Lep-MAP3, during the "2_create_genetic_map_lepmap.Rmd" script. It performed the second ordering of markers, computed for each chromosome separately and repeated 5 times. Markers which we...
application/x-shellscript - 1.1 KB - MD5: 12aebafffe6cfdff66ec056569d42193
Bash script used for submitting the job on the SGE cluster with "OrderMarkers2" function from Lep-MAP3, during the "2_create_genetic_map_lepmap.Rmd" script. It performed the third ordering of markers, computed for each chromosome separately and repeated 10 times. Markers which we...
application/x-shellscript - 1.2 KB - MD5: 2183a82e7c81a7ab0455580672546e21
Bash script used for submitting the job on the SGE cluster with "OrderMarkers2" function from Lep-MAP3, during the "2_create_genetic_map_lepmap.Rmd" script. It performed the last (fourth) ordering of markers, computed for each chromosome separately and repeated 20 times. Markers...
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