R Graphical Manual

Last data update: 2014.03.03

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Classification

Results 1 - 10 of 12 found.
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Les-class (Package: les) : Class 'Les'

The class 'Les' is used by the package 'les'.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: Les-class, [,Les-method, [<-,Les-method, show,Les-method, summary,Les-method
● 0 images

Les,ANY,numeric-method (Package: les) : Les

Constructs an object of class 'Les' and stores experimental tiling microarray data. This is the initial step for all further analysis with the 'les' package.

● Data Source: BioConductor
● Keywords: methods, utilities
● Alias: Les, Les,ANY,numeric-method, Les-methods
● 0 images

chi2,Les-method (Package: les) : chi2

The 'chi2' method can be used to optimize the window size for defined regions of interest. It computes chi^2(w) for window sizes w based on the estimates of Lambda and the false-discovery rate.

● Data Source: BioConductor
● Keywords: htest, methods
● Alias: chi2, chi2,Les-method, chi2-methods
● 1 images

ci,Les-method (Package: les) : ci

Computes confidence intervals (CI) for Lambda using bootstrapping.

● Data Source: BioConductor
● Keywords: htest, methods
● Alias: ci, ci,Les, ci,Les-method, ci-methods
● 1 images

estimate,Les-method (Package: les) : estimate

The 'estimate' method computes the fraction Lambda of probes with significant effect in the local surrounding of the genome.

● Data Source: BioConductor
● Keywords: htest, methods
● Alias: estimate, estimate,Les-method, estimate-methods
● 0 images

export,Les-method (Package: les) : export

Exports the results into files for interaction with other software. Estimated regions can be exported in 'bed' and 'gff' format, Lambda in 'wig' format.

● Data Source: BioConductor
● Keywords: IO, methods, utilities
● Alias: export, export,Les, export,Les-method, export-methods
● 0 images

les-internal (Package: les) :

Internal les functions

● Data Source: BioConductor
● Keywords: internal
● Alias: calcSingle, cdfDuplicates, checkState, fitGsri, ind2log, itLinReg, les-internal, log2ind, mcsapply, modGrenander, qrSlope, seFast, seSlopeWeight, setState, slopeWeight, wcdf2
● 0 images

les-package (Package: les) : Identifying Differential Effects in Tiling Microarray Data

The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

● Data Source: BioConductor
● Keywords: htest, package
● Alias: les, les-package
● 2 images

plot,Les-method (Package: les) : plot method for class Les

The 'plot' method plots the estimates of the 'les' package along the genome. This includeds Lambda with confidence intervals and estimated regions.

● Data Source: BioConductor
● Keywords: hplot, methods, utilities
● Alias: plot, plot,Les, plot,Les-method, plot-methods
● 1 images

regions,Les-method (Package: les) : regions

Estimates distinct regions of continuously elevated Lambda above a threshold Theta.

● Data Source: BioConductor
● Keywords: htest, methods
● Alias: regions, regions,Les, regions,Les-method, regions-methods
● 0 images