JMP Genomics Starter | Genetics | Other Association Testing

Other Association Testing
Click on a button corresponding to an association testing process not generally used for GWAS. Refer to the table below and the Comparison of Association Testing Processes for guidance.
Testing association between various types of traits and numerically coded genotypes from multiple SNPs at a time using logistic, linear, survival regression, and generalized linear mixed models on SNP genotypes themselves or principal components used to represent the SNP genotypes
Rare Variant Tutorial
Testing association between a trait or disease and rare variants, and optionally common variants, that occur in the same gene or pathway
Testing association between multiple traits (separately and jointly) and SNP genotypes or alleles from a single SNP at a time
Testing association between various types of traits and marker genotypes (using ANOVA) or alleles (using regression testing) from a single marker at a time, with many adjustments possible, including for Q and K matrices representing population structure and relatedness, respectively
Caution: This process can take an inordinate amount of time and computational resources. Consider choosing SNP-Trait Association when analyzing SNPs or multiallelic markers that can be treated as SNPs based on the most frequent allele.
Searching for pairs of SNPs predictive of a binary trait beyond the predictive ability of single SNPs, using penalized logistic regression (PLR)
Used to fit different combinations of Q and K variables and model fitness information from each model, such as AIC, AICC.
Note: You must already have computed the Q and K matrices.
See GWAS Testing for additional association testing processes.
See Genetics for other subcategories.