tni.constructor: A constructor for objects of class TNI.

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

This function is the main entry point of the TNI pipeline.

Usage

tni.constructor(expData, regulatoryElements, rowAnnotation=NULL, 
colAnnotation=NULL, cvfilter=FALSE, verbose=TRUE)

Arguments

expData	a gene expression matrix or 'SummarizedExperiment' object.
regulatoryElements	a vector of regulatory elements (e.g. transcription factors).
rowAnnotation	an optional data frame with gene annotation. Column 1 must provide all ids listed in the gene expression matrix. Ideally, col1 = <ID>, col2 = <GENEID>, and col3 = <SYMBOL>. Additional annotation can be included in the data frame and will be passed to the resulting TNI object. Furthermore, in order to eventually use the TNI object in AVS-class methods, it should also include chromosome coordinates: columns <CHROM>, <START> and <END>. Values in <CHROM> should be listed in [chr1, chr2, chr3, ..., chrX], while <START> and <END> correspond to chromosome positions (see avs.evse).
colAnnotation	an optional data frame with sample annotation.
cvfilter	a single logical value specifying to remove duplicated genes in the gene expression matrix using the probe-to-gene annotation. In this case, 'rowAnnotation' must be provided, with col1 = <ID> and col2 = <GENEID>. Genes duplicated in col2 will be collapsed; the decision is made based on the maximum dinamic range (i.e. keeping the gene with max coefficient of variation across all samples).
verbose	a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

A pre-processed TNI-class object.

Author(s)

Mauro Castro

See Also

TNI-class

Examples

data(tniData)

#--- run constructor
rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)

RTN documentation built on Nov. 12, 2020, 2:02 a.m.