notes/references.md

In variani/athaliana: Functions to work with the A. thaliana data set

Code examples with athaliana

• http://potatobreeding.cals.wisc.edu/wp-content/uploads/sites/21/2014/01/GWAS_tutorial.pdf

Articles related to athaliana

• http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001193#pgen.1001193-Platt1
• http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000843

Other data sets

• Mouse data http://mus.well.ox.ac.uk/mouse/HS/
  • artilce (pdf)

Sources

• http://www.nature.com/articles/ncomms5890

Mouse data. We used mouse data from Valdar et al.15 This data set contains between 1,700 and 1,940 samples (depending on phenotype missingness), 10,132 markers and 47 phenotypes.

Yeast data. We used yeast data from Bloom et al.25 This data set contains 1,008 samples, 11,623 markers and 46 phenotypes.

Human data. We used the data from Sabatti et al.26 and applied the same filtering criteria described in Zhou and Stephens17. This resulted in 5,255 individuals and 328,517 SNPs.

variani/athaliana documentation built on May 3, 2019, 4:34 p.m.