bnInfo: Constructing object of class bnInfo

In bnClustOmics: Bayesian Network-Based Clustering of Multi-Omics Data

Constructing object of class bnInfo

Description

This function constructs an object of class bnInfo which is needed for Bayesian network based clustering; see function bnclustOmics. In this object the names and types of omics data are stored as well as maappings containing the correspondance between gene names in each omic type and gene names used in blacklist and edge penalization matrices in the clustering step. These mappings are helpful for constructing such matrices. For example, transcriptome data often includes ensemble IDs and mutation data includes gene names. If we want to penalize all interactions which are not found in a specific interactions database, we need to pass an interaction list this list usually includes gene names and not ensemble IDs. Mappings pass the information needed to assign the edges between any IDs of gene X the specified penalization factor. If some omics types already have the same ID as in interaction list, corresponding mappings can be skipped.

Usage

bnInfo(omicdata, types, omics, mappings = NULL, attachtype = FALSE)

Arguments

omicdata	a list of matrices containing data, rows are observations, columns are variables (the order should be as following binary->ordinal->continuous)
types	a vector of characters equal in length to the number of provided omic matrices, "b" binary, "o" ordinal, "c" continuous
omics	a vector of omic names, must be the same as names of elements in omicdata, otherwise names of omicdata will be overwritten
mappings	mappings containing a gene symbol for each omic type, rownames have to contain column names of the parameter 'omicdata'; column "gene" must be present; if NULL for a certain omic type, than gene name will be taken from the column name of the corresponding matrix.
attachtype	when TRUE .O will be attached to each variable name, where O is omic name (see parameter 'omics'); when FALSE (default) .O is only attached to duplicated names

Value

an object of class bnInfo

Examples

#with mappings
bnnames<-bnInfo(toydata,c("b","o","c","c","c"),c("M","CN","T","P","PP"),mappings)
#no mappings
bnnames<-bnInfo(simdata,c("b","c"),c("M","T"))

bnClustOmics documentation built on Aug. 5, 2022, 5:11 p.m.