regions: regions

In les: Identifying Differential Effects in Tiling Microarray Data

Description

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

Usage

regions(object, limit=NULL, minLength=2, maxGap=Inf, verbose = FALSE,
...)

## S4 method for signature 'Les'
regions(object, limit=NULL, minLength=2, maxGap=Inf,
verbose = FALSE, ...)

Arguments

object	Object of class 'Les' as returned by 'threshold'.
limit	Numeric specifying the threshold Theta for Lambda with regions are defined as Lambda>=Theta (default: NULL). If 'NULL' Theta will be derived from the estimated number of regulated probes as computed by 'threshold'.
minLength	Integer specifying the minimum number of probes in a region (default: 2).
maxGap	Integer specifying maximum gap in base pairs between two neighboring probes in a region (default: Inf). If this value is exceeded the region will be split into smaller ones such that one region does not have neighboring probes with larger distance than 'maxGap'. If not specified arbitrary large gap sizes are allowed.
verbose	Logical indicating whether a summary of the estimated regions should be printed on screen (default: FALSE).
...	Further arguments passed to subsequent functions.

Details

This method finds distinct regions in Lambda by thresholding with Theta. The regions have to meet the following criteria:

(1) For all probes in the region Lambda>=Theta has to hold. (2) Each region has to contain at least as many probes as specified in 'minLength'. (3) The gap between to neighboring probes has to be smaller or equal to 'maxGap'.

Along with the boundaries of the regions the number of regulated probes within each region is estimated. This is used to sort the regions in order to get a list of top regions. The resulting data frame containing the regions can be accessed with the '[' method.

Value

Object of class 'Les' with additionally filled slots: regions, limit

'regions' is a data frame with variables:

chr	Chromosome the regions is located on.
start	Position of the beginning of the region.
end	Position of the end of the region.
size	Extend of the region in base pairs (measured in the same units as input 'pos', normally base pairs).
nProbes	Number of probes in the region.
ri	Regulation Index of the region indicating the fraction of regulated probes in the region.
se	Standard error of the estimation of 'ri'.
rs	Regulation score defined as 'ri'/'se'. The data frame is sorted according to this variable.

Author(s)

Julian Gehring

Maintainer: Julian Gehring <[e-mail]>

See Also

Package: les-package

Class: Les

Methods and functions: Les estimate threshold regions ci chi2 export plot

Examples

data(spikeInStat)

x <- Les(pos, pval)
x <- estimate(x, win=200)
x <- threshold(x, grenander=TRUE, verbose=TRUE)
x <- regions(x, verbose=TRUE)

print(x["regions"])

les documentation built on Nov. 8, 2020, 5:17 p.m.