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User Guide for ShiNyP: SNP Analysis and Visualization Platform

7 Core Collection

➡️ This section includes two subpages: Core Sample Set, and Core SNP Set, allowing you to capture the key samples and SNPs.

7.1 Core Sample Set

Establish a core collection that represents the genetic variation of the entire population. This approach is modified function from GenoCore (Jeong et al. 2017).

Required File:

  • data.frame

Steps:

  1. Choose the minimum genetic coverage (%).
  2. Choose the minimum genetic coverage differences between iterations.
  3. Click Run Core Sample to perform core collection.

Outputs:

  • Core Sample Coverage Data (CSV): A table listing the coverage (%) of each iteration and coverage differences between iterations.
  • Core Sample Set (RDS): A data.frame of core samples and their genotypic information.
  • Core Sample Info. (CSV): A table listing whether each sample is included in the core collection or not, and can be used as input data in the Population Structure/PCA subpage.
  • Coverage Plot of Core Sample Set (PDF): Visualizes the sample coverage by each iteration.

7.2 Core SNP Set

Establish a core SNP collection that represents the genetic variation observed in the full dataset or a random SNP set.

Required Files:

  • data.frame

  • Site Info. (RDS) of the current data.frame, downloadable from Data Input or Data QC pages

  • Chromosome Info. (CSV): Reference genome information of the current study. For more details about this file, refer to Section 2.3 (SNP Density).

    Download an example of Chromosome Info. (CSV).

  • DAPC Object (DAPC_dapc_Object.rds), downloadable from Population Structure/DAPC subpage.

Steps:

  1. Upload required datasts: Site Info. (RDS) and Chromosome Info. (CSV).
  2. Choose the method and Upload DAPC Object (RDS) or set the parameter.
  3. Click the Run Core SNP to perform core collection.

Outputs:

  • Core SNP Set (RDS): A data.frame of core SNPs and their genotypic information.
  • Core SNP Info. (RDS): A table listing whether each SNP is included in the core collection or not.
  • Distribution of Core SNPs (PDF): An ideogram labeling the core SNPs.
  • Site Info. of Core SNPs (RDS): Core SNPs site information file.