skcm.list

A dataset containing the processed inputs used in the melanoma analysis within the CRSO publication.

datasets

An algorithm for identifying candidate driver combinations in cancer. CRSO
is based on a theoretical model of cancer in which a cancer rule
is defined to be a collection of two or more events (i.e., alterations) that are minimally
sufficient to cause cancer. A cancer rule set is a set of cancer rules that collectively
are assumed to account for all of ways to cause cancer in the population. In CRSO every
event is designated explicitly as a passenger or driver within each patient.
Each event is associated with a patient-specific, event-specific passenger penalty,
reflecting how unlikely the event would have happened by chance, i.e., as a passenger.
CRSO evaluates each rule set by assigning all samples to a rule in the rule set,
or to the null rule, and then calculating the total statistical penalty from all
unassigned event. CRSO uses a three phase procedure find the best rule set of
fixed size K for a range of Ks. A core rule set is then identified from among
the best rule sets of size K as the rule set that best balances rule set size and
statistical penalty.
Users should consult the 'crso' vignette for an example walk through of a full CRSO run.
The full description, of the CRSO algorithm is presented in:
Klein MI, Cannataro V, Townsend J, Stern DF and Zhao H. "Identifying combinations of cancer driver in individual patients."
BioRxiv 674234 [Preprint]. June 19, 2019. <doi:10.1101/674234>.
Please cite this article if you use 'crso'.

Michael Klein

crso

Cancer Rule Set Optimization ('crso')

skcm.list function

A list with 3 items<dl class="dl-horizontal">
 <dt>D</dt><dd>Binary alteration matrix. Rows are candidate driver events, columns are samples.</dd>
 <dt>P</dt><dd>Passenger probability matrix corresponding to D.</dd>
 <dt>cnv.dictionary</dt><dd>Data frame containing copy number genes.</dd>
 ...
</dl>

Format

Example data set derived from TCGA skin cutaneous melanoma (SKCM) data. — skcm.list

A list with 3 items<dl class='dl-horizontal'>
 <dt>D</dt><dd>Binary alteration matrix. Rows are candidate driver events, columns are samples.</dd>
 <dt>P</dt><dd>Passenger probability matrix corresponding to D.</dd>
 <dt>cnv.dictionary</dt><dd>Data frame containing copy number genes.</dd>
 ...
</dl>

skcm.list: Example data set derived from TCGA skin cutaneous melanoma (SKCM) data.

Description

Usage

Arguments

Format