Genetic Association with JMP Genomics

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JMP Genomics is a specialized yet broad tool for analyzing genetic, genomic and other “-omic” data.

Whether it's expression analysis, GWAS, predictive modeling, or plant breeding, JMP Genomics has a tool to meet the need.

This blog series covers genetic association, beginning with the data import and continuing through several analytical pipelines.

Links to each of the nine blog posts can be accessed here as they become available. This week’s installment is Genetic Association with JMP Genomics, Part 1: Importing and Cleaning Data, and covers importing a series of .txt files into JMP, transposing and merging data sets, and prepping marker data for analysis.

Series Outline

Import

1. Genetic Association with JMP Genomics, Part 1: Importing and Cleaning Data
   
   1. Import EDF and Marker data
   2. Transposing and merging
   3. Recode Missing
   4. Numeric Genotypes
   5. Import Annotation

Basic Genetic Workflow

2. Genetic Association with JMP Genomics, Part 2: Basic Genetics Workflow (Case-Control)
   1. Marker Statistics
   2. Marker Properties
   3. Case-Control

Q-K Mixed Model

3. Genetic Association with JMP Genomics, Part 3a: Marker Based Relationship Matrix

1. K Matrix Compression

4. Genetic Association with JMP Genomics, Part 3b: Population Structure Matrix
5. Genetic Association with JMP Genomics, Part 3c: Q-K Mixed Model
6. Genetic Association with JMP Genomics, Part 3d: Q-K Mixed Model Workflow for Genetic Association
   1. PCA and Population Structure Matrix
   2. Relationship Matrix from Marker Data
   3. Q-K Mixed Model

Linkage Mapping and QTL

7. Genetic Association with JMP Genomics, Part 4: Basic Linkage Mapping
8. Genetic Association with JMP Genomics, Part 5: QTL Single Marker Analysis

GWAS

9. Genetic Association with JMP Genomics, Part 6: SNP-Trait Association