Canine atopic dermatitis datasets
type: Dataset
description: 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).
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Katarina Tengvall
date modified: 2023-06-05
date published: 2022-11-09
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Genetics and Genomics
  type: DefinedTerm
  term code: 10609
keywords: Gene mapping
license: https://creativecommons.org/licenses/by/4.0/
publisher: Uppsala University
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.21287139

Katarina Tengvall
type: Person
affiliation: Science for Life Laboratory
family name: Tengvall
given name: Katarina

Science for Life Laboratory
type: Organization

Uppsala University
type: Organization