Canine atopic dermatitis datasets

The datasets consists of genotype data from dogs in plink format. ATOPYK2 plink files contains genotype data from five dog breeds with and without atopic dermatitis. The ATOPYK2 datafiles were used for imputation. These are pre-QC:ed with the following plink settings --maf 0.001 --geno 0.05 --mind 0.05 #We recommend a second qc before doing the imputation. The imputation was then run per chromosome so for redoing the imputation, as was done in the publication to which this data is connected, use the following plink code: plink --bfile ATOPYK2 --chr $chrN --make-bed --dog --allow-no-sex --keep-allele-order --maf 0.001 --geno 0.2 --out 'ATOPYK.chr'$chrN #The final datasets after imputation are datasets split breed wise and in plink format. These sets are QC:ed, and relatedness filtered. The "covar"-file includes fixed effects, these are different between depending on what covariates were significantly affecting the trait (atopic dermatitis) in each breed. These datasets are named GR (golden retriever), LR (labrador retriever), GSD (german shepherd) and WHWT (west highland white terrier). (Boxers are in the ATOPYK2 files but not used for final analyses, hence no breed specific datafile for boxer are included).

本数据集包含PLINK格式（PLINK）的犬类基因型数据。ATOPYK2 PLINK文件涵盖了5个犬品种的基因型数据，对应个体是否患有特应性皮炎（atopic dermatitis）。
ATOPYK2数据集文件曾用于基因型填充（imputation）。该数据集已完成初步质控，质控参数为：--maf 0.001 --geno 0.05 --mind 0.05。我们建议在开展基因型填充前再次执行质控步骤。
后续将按染色体进行基因型填充，若需复现该数据集关联论文中的分析流程，可使用如下PLINK代码：
plink --bfile ATOPYK2 --chr $chrN --make-bed --dog --allow-no-sex --keep-allele-order --maf 0.001 --geno 0.2 --out 'ATOPYK.chr'$chrN
基因型填充完成后的最终数据集按犬品种拆分，仍采用PLINK格式存储。这些数据集均已完成质控与亲缘关系过滤。其中的"covar"文件包含固定效应变量，其具体组成因不同犬品种中对特应性皮炎性状存在显著影响的协变量而异。
本数据集包含四个品种的专属文件：GR（金毛寻回犬，Golden Retriever）、LR（拉布拉多寻回犬，Labrador Retriever）、GSD（德国牧羊犬，German Shepherd）以及WHWT（西部高地白㹴，West Highland White Terrier）。拳师犬（Boxer）仅包含于ATOPYK2原始文件中，未纳入最终分析，因此未提供其品种专属数据集。