Class 'Les'

Description

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

Objects from the Class

Objects of class 'Les' are constructed by calling the function 'Les'.

Slots

pos:

Integer vector with probe positions. Provided by the user through the 'Les' function.

chr:

Factor with chromosomes for each probe. Provided by the user through the 'Les' function.

lambda:

Numeric vector with estimates Lambda for each probe.

lambda0:

Numeric vector with estimates Lambda0 without the Grenander estimator for each probe. This is used if 'grenander' is set to TRUE.

se:

Numeric vector with standard error from linear fitting for each probe.

nProbes:

Integer with number of probes used in fit for each probe

pval:

Numeric vector with p-values for each probe. Provided by the user through the 'Les' function.

win:

Integer with the window size. Set by the user in the 'estimate' function.

weighting:

Function with the weighting function used for probe weighting according to position. Set by the user in the 'estimate' function.

grenander:

Logical indicating usage of the Grenander estimator. Set by the user in the 'estimate' function.

ci:

Data frame with the confidence intervals for each probe specified in 'subset'.

nBoot:

Integer with the number of bootstraps to be drawn. Set by the user in the 'ci' function.

conf:

Numeric with the confidence level. Set by the user in the 'ci' function.

subset:

Integer vector with indices of bootstrap subset. Set by the user in the 'ci' function.

theta:

Numeric with the threshold value Theta.

nSigProbes:

Integer with the number of estimated significant probes.xs

regions:

Data frame with estimated Loci of Enhanced Significance.

limit:

Numeric with the threshold value for estimation of 'regions'. Set by the user in the 'regions' function.

nChr:

Integer with the number of chromosomes.

maxGap:

Numeric specifying the largest gap allowed in one region. Set by the user in the 'regions' function.

minLength:

Integer specifying the minimal number of probes in one region. Set by the user in the 'regions' function.

minProbes:

Integer specifying the minimal number of unique p-values allowed for each fit. Set by the user in the 'estimate' function.

method:

Character specifying the method used for linear regression.

winSize:

Integer vector specifying the window sizes used for chi2 computation.

chi2:

Matrix containing the chi2 values for different window sizes.

state:

Character vector containing the analysis steps applied on the data object. Used for internal consistency checks.

Author(s)

Julian Gehring

Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>

See Also

Package: les-package

Class: Les

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

Examples

showClass("Les")