.epsilon_matrix

Compute the epsilon matrix by permutation for the <code>sGBJ_scores()</code> function.

Implements an extension of the Generalized Berk-Jones (GBJ) statistic for
survival data, sGBJ. It computes the sGBJ statistic and its p-value for testing
the association between a gene set and a time-to-event outcome with possible
adjustment on additional covariates. Detailed method is available at Villain L, Ferte T,
Thiebaut R and Hejblum BP (2021) <doi:10.1101/2021.09.07.459329>.

Laura Villain

sGBJ

Survival Extension of the Generalized Berk-Jones Test

Thomas Ferte

Rodolphe Thiebault

Boris P. Hejblum

.epsilon_matrix function

<dl><dt>Z</dt>
<dd>the score vector returned by <code>.survival_scores()</code> function.</dd>
<dt>nperm</dt>
<dd>number of permutations performed to estimate the <code>epsilon</code> matrix.
Default is <code>300</code>.</dd>
<dt>surv</dt>
<dd>a <code><a href="/link/Surv?package=sGBJ&version=0.1.1" data-mini-rdoc="sGBJ::Surv">Surv</a></code> object of length <code>n</code></dd>
<dt>factor_matrix</dt>
<dd>a <code>n x p</code> <code>data.frame</code> of the expression for the
particular gene set of interest being tested</dd>
<dt>covariates</dt>
<dd>a <code>n x l</code> matrix of the covariates to adjust upon. Default is <code>NULL</code></dd>
<dt>dat</dt>
<dd>data used to fit survival model returned by <code>.survival_scores()</code> function.</dd></dl>

Arguments

.epsilon_matrix — .epsilon_matrix

<dl>

<dt>Z</dt>
<dd>the score vector returned by <code>.survival_scores()</code> function.</dd>


<dt>nperm</dt>
<dd>number of permutations performed to estimate the <code>epsilon</code> matrix.
Default is <code>300</code>.</dd>


<dt>surv</dt>
<dd>a <code><a href='https://rdrr.io/pkg/survival/man/Surv.html'>Surv</a></code> object of length <code>n</code></dd>


<dt>factor_matrix</dt>
<dd>a <code>n x p</code> <code>data.frame</code> of the expression for the
particular gene set of interest being tested</dd>


<dt>covariates</dt>
<dd>a <code>n x l</code> matrix of the covariates to adjust upon. Default is <code>NULL</code></dd>


<dt>dat</dt>
<dd>data used to fit survival model returned by <code>.survival_scores()</code> function.</dd>

</dl>

.epsilon_matrix: .epsilon_matrix

Description

Usage

Value

Arguments