Data on 1,307 Arabidopsis thaliana accessions collected around the world. Data include geographic co-ordinates and results of applying principal components analysis (PCA) to genotypes at 214,051 single nucleotide polymorphisms (SNPs).

data(regmap)

Format

regmap is a data frame with 1,307 rows and 21 columns, in which each row represents an A. thaliana accession included in the RegMap panel. The last 11 columns (labeled "PC1" through "PC10") store the projection of the samples onto the first 10 PCs.

Source

Arabidopsis thaliana SNP genotypes were obtained from the website of Joy Bergelson's lab at the University of Chicago, http://bergelson.uchicago.edu/?page_id=790.

Details

PCs were computed using rpca from the rsvd package after first converting the genotypes to a 1,307 x 214,051 binary matrix.

References

Horton, M. W., Hancock, A. M., Huang, Y. S., Toomajian, C., Atwell, S., Auton, A., et al (2012). Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44, 212–216.

Examples

# View the first few data samples. data(regmap) head(regmap)
#> array_id ecotype_id median_intensity latitude longitude nativename firstname #> 1 641 9381 476 55.8106 14.2091 Fri 1 Alison #> 2 642 9380 556 55.7488 13.3742 FlyA 3 Alison #> 3 643 9378 542 63.0165 18.3174 FaU 4 Alison #> 4 644 9371 478 63.0160 18.3175 FaL 1 Alison #> 5 645 9367 560 57.6787 14.9981 EkN 3 Alison #> 6 646 9363 363 62.9147 18.4045 EdJ 2 Alison #> surname site region country PC1 PC2 PC3 PC4 #> 1 Anastasio Frisaboda S Sweden SWE -27.7564 34.4838 6.2580 -2.0400 #> 2 Anastasio Flyinge S Sweden SWE -20.1760 34.9538 15.6064 -6.1097 #> 3 Anastasio Faberget-Upper N Sweden SWE -56.7601 89.7009 9.0919 11.4833 #> 4 Anastasio Faberget-Lower N Sweden SWE -55.6441 88.5797 8.0689 9.9808 #> 5 Anastasio Eksjoholm-Norra C Sweden SWE -38.5506 6.1973 -6.9958 -5.7941 #> 6 Anastasio Edsattersjon N Sweden SWE -60.6846 109.8771 16.1302 13.5530 #> PC5 PC6 PC7 PC8 PC9 PC10 #> 1 -6.5748 -1.4439 2.2803 25.6212 -10.9108 18.6137 #> 2 -99.2813 -44.4414 -38.4179 -40.0077 24.6401 6.5482 #> 3 46.6343 -1.4997 0.0836 -14.2385 -3.0902 -6.1308 #> 4 46.1855 -1.2229 1.5694 -15.3463 -2.3640 -4.1847 #> 5 -12.8444 1.4173 5.9657 23.0560 -3.2038 -23.0929 #> 6 46.3648 -2.1523 -10.4390 -20.7712 10.2359 -1.0296
# NOT RUN { # See the vignette for more examples. vignette("regmap") # }