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