fishers_combined

This function takes in the p-values tibble that mvmapit returned. It then
computes the combined p-values grouped by variant id.

Epistasis, commonly defined as the interaction between genetic
loci, is known to play an important role in the phenotypic variation of
complex traits. As a result, many statistical methods have been developed to
identify genetic variants that are involved in epistasis, and nearly all of
these approaches carry out this task by focusing on analyzing one trait at a
time. Previous studies have shown that jointly modeling multiple phenotypes
can often dramatically increase statistical power for association mapping. In
this package, we present the 'multivariate MArginal ePIstasis Test'
('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic
detection method which seeks to detect marginal epistasis or the combined
pairwise interaction effects between a given variant and all other variants.
By searching for marginal epistatic effects, one can identify genetic variants
that are involved in epistasis without the need to identify the exact
partners with which the variants interact – thus, potentially alleviating
much of the statistical and computational burden associated with conventional
explicit search based methods. Our proposed 'mvMAPIT' builds upon this
strategy by taking advantage of correlation structure between traits to
improve the identification of variants involved in epistasis.
We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a
multi-trait variance component estimation algorithm for efficient parameter
inference and P-value computation. Together with reasonable model
approximations, our proposed approach is scalable to moderately sized
genome-wide association studies.
Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>.
Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.

Julian Stamp

mvMAPIT

Multivariate Genome Wide Marginal Epistasis Test

Lorin Crawford

fishers_combined function

<dl><dt>pvalues</dt>
<dd>Tibble with p-values from mvmapit function call.</dd>
<dt>group_col</dt>
<dd>String that denotes column by which to group and combine
p-values.</dd>
<dt>p_col</dt>
<dd>String that denotes p-value column.</dd></dl>

Arguments

Fisher's combine method on mvmapit return — fishers_combined

<dl>

<dt>pvalues</dt>
<dd>Tibble with p-values from mvmapit function call.</dd>


<dt>group_col</dt>
<dd>String that denotes column by which to group and combine
p-values.</dd>


<dt>p_col</dt>
<dd>String that denotes p-value column.</dd>

</dl>

fishers_combined: Fisher's combine method on mvmapit return

Description

Usage

Value

Arguments

Examples