GenometriCorrResult-class: The class contains the results of the GenometriCorrelation...

In favorov/GenometriCorr: Genometric Correlation package

Description

The GenometriCorrResult-class is generated by GenometriCorrelation or GenometriCorr:::run.config; it is inherited from a namedList that contains the list of results. Three mechanisms, print, graphical.report, and visualize create text and/or graphics that summarize the results in a human-readable way.

Creating Objects

new('GenometriCorrConfig',src)
The object is generated by GenometriCorrelation or GenometriCorr:::run.config;

Slots

.Data:

Object of class "list" ~~

config:

Object of class "GenometriCorrConfig" ~~

names:

Object of class "character" ~~

Slots

.Data

The result of the GenometriCorrelation call. It is a list and the names slot contains the names of the members of the result list.

config

The config in an instance of GenometriCorrConfig-class class that stores the parameters that were used in the GenometriCorrelation run that gave the results.

names:

Object of class "character"; names of the resulting list; it saves of the spaces (chromosomes) used for the calculations. It is inherited from "namedList"

Extends

Class "namedList", directly. Class "list", by class "namedList", distance 2. Class "vector", by class "namedList", distance 3.

Methods

show

signature(object = "GenometriCorrResult"): writes the results as plain text.

graphical.report

signature(x = "GenometriCorrResult"):
graphical.report(result,pdffile,show.all,show.chromosomes,trustname,make.new)plots the results as a pdf, named pdffile. If a filename is not given, it creates the filename from the original datafile names. show.all is a boolean, determining whether to show graphics for all chromosomes as well as the summary statistics for all data (default is TRUE). If FALSE, only the summary statistics for all data will appear in the output. chromosomes.to.show lists which individual chromosome results should be in the output; in this case the summary statistics for all data will not be shown. Default is ("").If trustname is TRUE it does not try to add a .pdf extension to the filename supplied.

visualize

signature(x = "GenometriCorrResult"):
visualize(result,pdffile,show.all,show.chromosomes,trustname,make.new)behaves much like the graphical.report function but generates a pdf with a full graphical overview. pdffile, show.all, and chromosomes.to.show behave as for graphical.report. style is a string with the name of the color style. Currently, only two are available: "blue-white-red" (default) and "rainbow" (the old one). The graphical overview depicts both data density and the significance of trends in the spatial relationship between query and reference data.

Author(s)

Alexander Favorov [e-mail], Loris Mularoni, Yulia Medvedeva, Harris A. Jaffee, Ekaterina V. Zhuravleva, Veronica Busa, Leslie M. Cope, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan

References

http://genometricorr.sourceforge.net/

See Also

The GenometriCorrResult-class class; the GenometriCorr documentation and the GenometriCorr package vignette.

Examples

library("GenometriCorr")

cpgis_bed<-system.file("extdata", "UCSCcpgis_hg19.bed", package = "GenometriCorr");

refseq_bed<-system.file("extdata", "UCSCrefseqgenes_hg19.bed", package = "GenometriCorr");

config<-new("GenometriCorrConfig",system.file("extdata","template-config.ini", package = "GenometriCorr"))
#creating the new config from the template-config.ini

config$tests$permut.number=10

#sets all permutation numbers to 10

config$options$showTkProgressBar=FALSE
#suppresss the Tk progress bar

print(config)
#printing the changed file back, just to see it 

result<-run.config(config,query=cpgis_bed,reference=refseq_bed)
#running GenometriCorrelation with the parameters from config
#and query and reference file names as given

print(result)

graphical.report(result)

favorov/GenometriCorr documentation built on March 30, 2021, 5:21 p.m.