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.
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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
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Rare Variant Tutorial
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Testing association between a trait or disease and
rare variants
, and optionally common variants, that occur in the same gene or pathway
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Testing association between
multiple traits
(separately and jointly) and SNP genotypes or
alleles
from a
single SNP at a time
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|
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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.
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Searching for pairs of SNPs predictive of a
binary trait
beyond the predictive ability of single SNPs, using
penalized logistic regression
(PLR)
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Used to fit different combinations of Q and K
variables
and
model
fitness information from each model, such as AIC, AICC.
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See
GWAS Testing
for additional association testing processes.