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).

本数据集包含采用PLINK（PLINK）格式存储的犬类基因型数据。

ATOPYK2的PLINK文件包含5个犬品种的基因型数据，对应个体分别患有或未患有特应性皮炎（atopic dermatitis）。该数据集曾被用于基因型填充（imputation），并已通过以下PLINK参数完成预质控：--maf 0.001 --geno 0.05 --mind 0.05。

# 我们建议在开展基因型填充前执行第二次质控。本次基因型填充按染色体分批次运行，若需复刻本数据集关联的已发表文献中的填充流程，请使用以下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为按品种拆分的PLINK（PLINK）格式数据集。这些数据集均已完成质控并过滤了亲缘关系样本。其中的"协变量文件（covar-file）"包含固定效应项；由于不同品种中对特应性皮炎性状存在显著影响的协变量存在差异，各品种对应的固定效应项也各不相同。本数据集按品种命名为：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）。（拳师犬的样本包含于ATOPYK2文件中，但未用于最终分析，因此未提供对应品种的专属数据集文件。）