Les-class: Class 'Les'

In les: Identifying Differential Effects in Tiling Microarray Data

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 <[e-mail]>

See Also

Package: les-package

Class: Les

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

Examples

showClass("Les")

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