les (version 1.22.0)

regions,Les-method: regions

Description

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

Usage

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

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.

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.

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"])