regmappcs: Principal components of RegMap data on A. thaliana

In xinghuq/KLFDAPC: KLFDAPC: Kernel Local Fisher Discriminant Analysis of Principal Components- A Non-linear Tool for Population Structure Inference.

Principal components of RegMap data on A. thaliana

Description

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). This data is obtained from Novembre, et al.2008.See PCAviz package.

Usage

data("regmappcs")

Format

regmappcs 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.

Details

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

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. We used the data from Novembre, et al.2018 PCAviz package.

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. Novembre, J., R. Williams, H. Pourreza, Y. Wang, and P. Carbonetto.(2018) "PCAviz: Visualizing principal components analys." R Package.

Examples

# View the first few data samples.
data(regmappcs)
head(regmappcs)

## Not run: 
# See the vignette for more examples.
vignette("regmappcs")

## End(Not run)

xinghuq/KLFDAPC documentation built on June 12, 2022, 7:20 p.m.