tni.constructor {RTN} | R Documentation |
This function is the main entry point of the TNI pipeline.
tni.constructor(expData, regulatoryElements, rowAnnotation=NULL, colAnnotation=NULL, cvfilter=TRUE, verbose=TRUE)
expData |
a gene expression matrix or 'SummarizedExperiment' object. |
regulatoryElements |
a vector of regulatory elements (e.g. transcription factors). |
rowAnnotation |
an optional data frame or matrix with probe-to-gene annotation (e.g. probe-to-gene information). Column 1 must provide all probe ids listed in the 'gexp' matrix. Ideally, col1 = <PROBEID>, 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 |
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 = <PROBEID> and col2 = <GENEID>. The decision is made based on the maximum dinamic range (i.e. keeping the probes 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). |
Mauro Castro
data(dt4rtn) #--- select 5 regulatoryElements to illustrate the constructor tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")] #--- run constructor rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test, rowAnnotation=dt4rtn$gexpIDs)