PMatrix-class

PMatrix

[,PMatrix,matrix,missing,ANY-method

[,PMatrix,missing,numeric,ANY-method

[,PMatrix,numeric,missing,ANY-method

[,PMatrix,numeric,numeric,ANY-method

dim,PMatrix-method

An S4 class to store the probabilities of gene i being mutated in sample j

An optimized method for identifying mutually
exclusive genomic events. Its main contribution is a
statistical analysis based on the Poisson-Binomial
distribution that takes into account that some samples
are more mutated than others. See [Canisius, Sander, John WM Martens,
and Lodewyk FA Wessels. (2016) "A novel independence test for
somatic alterations in cancer shows that
biology drives mutual exclusivity but chance explains
most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>].
The mutations matrices are sparse matrices. The method developed takes
advantage of the advantages of this type of matrix to save
time and computing resources.

Juan A. Ferrer-Bonsoms Developer

Rediscover

Identify Mutually Exclusive Mutations

Juan A. Ferrer-Bonsoms

Laura Jareno

Angel Rubio

PMatrix-class function

<dl>
<dt><code>rowExps</code></dt>
<dd>Sample depending estimated coefficients obtained from the logistic regression</dd><dt><code>colExps</code></dt>
<dd>gene depending estimated coefficients obtained from the logistic regression</dd>
</dl>

Slots

An S4 class to store the probabilities — PMatrix-class

<dl>
<dt><code>rowExps</code></dt>
<dd>Sample depending estimated coefficients obtained from the logistic regression</dd>

<dt><code>colExps</code></dt>
<dd>gene depending estimated coefficients obtained from the logistic regression</dd>


</dl>

An S4 class to store the probabilities

PMatrix-class: An S4 class to store the probabilities

Description

Arguments

Slots