kernTEST

Perform optimal transport on somatic point mutations and kernel regression hypothesis testing by integrating pathway level similarities at the gene level (Little et al. (2023) <doi:10.1111/biom.13769>). The software implements balanced and unbalanced optimal transport and omnibus tests with 'C++' across a set of tumor samples and allows for multi-threading to decrease computational runtime.

Paul Little

ROKET

Optimal Transport-Based Kernel Regression

kernTEST function

<dl><dt>RESI</dt>
<dd>A numeric vector of null model residuals
<code>names(RESI)</code> must be set to maintain sample ordering
for survival regression, otherwise set <code>RESI</code> to <code>NULL</code>.</dd>
<dt>KK</dt>
<dd>An array containing double-centered positive semi-definite
kernel matrices. Refer to <code>MiRKAT::D2K()</code> for transforming 
distance matrices to kernel matrices. The <code>dimnames(KK)[[1]]</code> and 
<code>dimnames(KK)[[2]]</code> must match <code>names(RESI)</code>.
Also set dimnames(KK)[[3]] to keep track of each kernel matrix.</dd>
<dt>YY</dt>
<dd>A numeric vector of continuous outcomes to be fitted
in a linear model. Defaults to NULL for survival model.</dd>
<dt>XX</dt>
<dd>A numeric data matrix with first column for intercept,
a column of ones.</dd>
<dt>OMNI</dt>
<dd>A matrix of zeros and ones. Each column corresponds to a
distance matrix while each row corresponds to an omnibus test. Set
<code>rownames(OMNI)</code> for labeling outputted p-values and 
<code>colnames(OMNI)</code> which should match <code>dimnames(KK)[[3]]</code>.</dd>
<dt>nPERMS</dt>
<dd>A positive integer to specify the number of
permutation-based p-value calculation</dd>
<dt>ncores</dt>
<dd>A positive integer for the number of cores/threads
to reduce computational runtime when running for loops</dd></dl>

Arguments

kernTEST — kernTEST

<dl>

<dt>RESI</dt>
<dd>A numeric vector of null model residuals
<code>names(RESI)</code> must be set to maintain sample ordering
for survival regression, otherwise set <code>RESI</code> to <code>NULL</code>.</dd>


<dt>KK</dt>
<dd>An array containing double-centered positive semi-definite
kernel matrices. Refer to <code>MiRKAT::D2K()</code> for transforming 
distance matrices to kernel matrices. The <code>dimnames(KK)[[1]]</code> and 
<code>dimnames(KK)[[2]]</code> must match <code>names(RESI)</code>.
Also set dimnames(KK)[[3]] to keep track of each kernel matrix.</dd>


<dt>YY</dt>
<dd>A numeric vector of continuous outcomes to be fitted
in a linear model. Defaults to NULL for survival model.</dd>


<dt>XX</dt>
<dd>A numeric data matrix with first column for intercept,
a column of ones.</dd>


<dt>OMNI</dt>
<dd>A matrix of zeros and ones. Each column corresponds to a
distance matrix while each row corresponds to an omnibus test. Set
<code>rownames(OMNI)</code> for labeling outputted p-values and 
<code>colnames(OMNI)</code> which should match <code>dimnames(KK)[[3]]</code>.</dd>


<dt>nPERMS</dt>
<dd>A positive integer to specify the number of
permutation-based p-value calculation</dd>


<dt>ncores</dt>
<dd>A positive integer for the number of cores/threads
to reduce computational runtime when running for loops</dd>

</dl>

kernTEST: kernTEST

Description

Usage

Value

Arguments