rHVDM (version 1.38.0)

HVDMreport: generates an HTML report using the input

Description

This method generates report using one of the HVDM outputs (either from the training(), screeening() or fitgene() commands.)

Usage

HVDMreport(HVDM,name)

Arguments

HVDM

a list output either by a training(), screening() or fitgene() command.

name

an optional argument allowing to specify the name of the HTML file (the .HTML extension is added automatically).

Value

Nothing is returned, but a message indicating the name of the HTML file and its location on the hard drive is given.

Details

If the output has been generated by training() or fitgene(), the HTML report contains four sections: 1) Functions inputs. 2) Model score. 3) Fitted parameters. 4) Visual comparison of model and data. In the fitgene() case comparisons with correponding results for genes in the training set are given. If the output has been generated by the screening() command, the HTML report contains the following sections:

1) Inputs to the preceding training() command. 2) Inputs to the screening() command (such as bounds used to classify genes). 3) Results. 4) List of putative targets of the transcription factor under review. The HTML report is genereated in the current working directory. Graphic files are stored in a subdirectory with a similar name.

References

M. Barenco, D. Tomescu, D. Brewer, R. Callard, J. Stark, M. Hubank (2006) Ranked predictions of p53 targets using Hidden Variable Dynamic Modelling. Genome Biology, V7(3), R25.

See Also

training,screening,fitgene

Examples

data(HVDMexample)
tHVDMp53<-training(eset=fiveGyMAS5,genes=p53traingenes,degrate=0.8,actname="p53")
#HVDMreport(tHVDMp53)
#HVDMreport(tHVDMp53, name="p53training")