mapSTRING

A data frame containing mapping between names of genes used in <code>kirp</code>/<code>kirc</code>
data sets and names used in STRING interactions list (see <code><a rd-options="" href="/link/intSTRING?package=BiDAG&version=2.0.0" data-mini-rdoc="BiDAG::intSTRING">intSTRING</a></code>).

datasets

Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter and G. Moffa (2018) <arXiv:1803.07859v2>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.

Polina Suter

BiDAG

Bayesian Inference for Directed Acyclic Graphs

mapSTRING function

A data frame with 46 rows and two columns:<ul>
<li>queryItem character, name used for structure learning (for example see column names of <code><a rd-options="" href="/link/kirp?package=BiDAG&version=2.0.0" data-mini-rdoc="BiDAG::kirp">kirp</a></code>)</li>
<li>preferredName character, name used in STRING interactions data set (see <code><a rd-options="" href="/link/intSTRING?package=BiDAG&version=2.0.0" data-mini-rdoc="BiDAG::intSTRING">intSTRING</a></code>)</li>
</ul>

Format

A data frame containing mapping between names of genes used in <code>kirp</code>/<code>kirc</code>
data sets and names used in STRING interactions list (see <code><a rd-options='' href='intSTRING'>intSTRING</a></code>).

mapSTRING dataset — mapSTRING

A data frame with 46 rows and two columns:<ul>
<li>queryItem character, name used for structure learning (for example see column names of <code><a rd-options='' href='kirp'>kirp</a></code>)</li>
<li>preferredName character, name used in STRING interactions data set (see <code><a rd-options='' href='intSTRING'>intSTRING</a></code>)</li>
</ul>

mapSTRING: mapSTRING dataset

Description

Usage

Arguments

Format