| Maintainer: | Mathieu Gautier <mathieu.gautier@supagro.inra.fr> |
| Author: | Mathieu Gautier, Alexander Klassmann and Renaud Vitalis |
| Version: | 1.0.0 |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Title: | Data Only: Searching for Footprints of Selection using Haplotype Homozygosity Based Tests |
| Description: | Contains example data for the 'rehh' package. |
| Depends: | R (≥ 2.10) |
| NeedsCompilation: | no |
| Packaged: | 2016-11-07 17:07:09 UTC; mathieu |
| Repository: | CRAN |
| Date/Publication: | 2016-11-08 11:10:29 |
Data Only: Searching for Footprints of Selection using Haplotype Homozygosity Based Tests Description: Contains example data for the 'rehh' package.
Description
Contains example data for the package rehh.
Details
| Package: | rehh.data |
| Version: | 1.0.0 |
| License: | GPL(>=2) |
Index:
wgscan.cgu Whole genome scan results for the CGU
(Creole from Guadeloupe island)
wgscan.eut Whole genome scan results for a pool of
European taurine cattle
References
Gautier M., Klassmann A., and Vitalis R. (2016). rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Molecular Ecology Resources, submitted
Gautier M. and Vitalis R. (2012). rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, 28(8), 1176–1177.
Gautier, M. and Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128–3143.
Whole genome scan results for the CGU (Creole from Guadeloupe island)
Description
A dataframe object with of 44,057 rows (SNPs) and 7 columns: i) chromosome name (CHR), ii) position of the SNP in bp (POSITION), iii) Ancestral allele frequency (freq_A), iv) iHH for the ancestral allele (iHH_A), v) iHH for the derived allele (iHH_D), vi) iES using the estimator by Tang et al. (2007) (iES_Tang_et_al_2007), vii) iES using the estimator by Sabeti et al. (2007) (iES_Sabeti_et_al_2007).
Usage
data(wgscan.cgu)References
Gautier, M. and Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128–3143.
Whole genome scan results for a pool of European taurine cattle
Description
A dataframe object with 44,057 rows (SNPs) and 7 columns: i) chromosome name (CHR), ii) position of the SNP in bp (POSITION), iii) Ancestral allele frequency (freq_A), iv) iHH for the ancestral allele (iHH_A), v) iHH for the derived allele (iHH_D), vi) iES using the estimator by Tang et al. (2007) (iES_Tang_et_al_2007), vii) iES using the estimator by Sabeti et al. (2007) (iES_Sabeti_et_al_2007).
Usage
data(wgscan.eut)References
Gautier, M. and Naves, M. (2011). Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Molecular Ecology, 20, 3128–3143.