Les-class {les} | R Documentation |
The class 'Les' is used by the package 'les'.
Objects of class 'Les' are constructed by calling the function 'Les'.
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.
Julian Gehring
Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>
Package:
les-package
Class:
Les
Methods and functions:
Les
estimate
threshold
regions
ci
chi2
export
plot
showClass("Les")