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Function edrSelec [edrGraphicalTools v2.2]
keywords
nonlinear
title
Variable selection based on sliced inverse regression
description
Gathers several procedures to determine which explanatory variables have an effect on a dependent variable. Works whether there are more explanatory variables than observations or not. Creates an object of class edrSelec.
Function edrUnderdet [edrGraphicalTools v2.2]
keywords
nonlinear
title
EDR space estimation for underdetermined cases.
description
Gathers several procedures to estimate the effective dimension regression (EDR) space when the number of explanatory variables is greater than the sample size. Creates an object of class edr.
Function sliceMat [edrGraphicalTools v2.2]
keywords
nonlinear
title
Slicing matrix computation
description
Returns the slicing matrix required for the "SIR-I" method.
Function wavShrink [wmtsa v2.0-3]
keywords
nonlinear
title
Nonlinear denoising via wavelet shrinkage
description
Performs a decimated or undecimated discrete wavelet transform on the input series and "shrinks" (decreases the amplitude towards zero) the wavelet coefficients based on a calculated noise threshold and specified shrinkage function. The resulting shrunken set of wavelet transform coefficients is inverted in a synthesis operation, resulting in a denoised version of the original series.
Function refmean [qpcR v1.4-1]
keywords
nonlinear
title
Averaging of multiple reference genes
description
This function averages the expression of several reference genes before calculation of gene expression ratios by ratiocalc or ratiobatch. The method is similar to that described in Vandesompele et al. (2002), but uses arithmetic averaging of threshold cycles/efficiencies and not geometric averaging of relative expression values. This is equivalent, as discussed in 'Details' and as shown in 'Examples'. An essential extension of this method is, that if replicates for the reference genes are supplied, the threshold cycles and efficiencies are subjected to error propagation prior to ratio calculation. The propagated error is then included in the calculation of the gene expression ratios, as advocated in Nordgard et al. (2006).
Function ratioPar [qpcR v1.4-1]
keywords
nonlinear
title
Calculation of ratios in a batch format from external PCR parameters
description
Starting from external PCR parameters such as threshold cycles/efficiency values commonly obtained from other programs, this function calculates ratios between samples, using normalization against one or more reference gene(s), if supplied. By default, multiple reference genes are averaged according to Vandesompele et al. (2002). The input can be single qPCR data or (more likely) data containing replicates. It is similar to ratiobatch and can handle multiple reference genes and genes-of-interest with multiple (replicated) samples as found in large-scale qPCR runs such as 96- or 384-Well plates. The results are automatically stored as a file or copied into the clipboard. A boxplot representation for all Monte-Carlo simulations, permutations and error propagations including 95% confidence intervals is also given.
Function ratiobatch [qpcR v1.4-1]
keywords
nonlinear
title
Calculation of ratios in a batch format for multiple genes/samples
description
For multiple qPCR data from type 'pcrbatch', this function calculates ratios between samples, using normalization against one or more reference gene(s), if supplied. Multiple reference genes can be averaged according to Vandesompele et al. (2002). The input may be single qPCR data or (more likely) data containing replicates. This is essentially a version of ratiocalc that can handle multiple reference genes and genes-of-interest with multiple (replicated) samples as found in large-scale qPCR runs such as 96- or 384-Well plates. A boxplot representation for all Monte-Carlo simulations, permutations and error propagations including 95% confidence intervals is calculated for each ratio calculation.
Function ratiocalc [qpcR v1.4-1]
keywords
nonlinear
title
Calculation of ratios from qPCR runs with/without reference genes
description
For multiple qPCR data from type 'pcrbatch', this function calculates ratios between two samples (control/treatment) of a gene-of-interest, using normalization against a reference gene, if supplied. The input can be single qPCR data or (more likely) data containing replicates. Errors and confidence intervals for the obtained ratios can be calculated by Monte-Carlo simulation, a permutation approach similar to the popular REST software and by error propagation. Statistical significance for the ratios is calculated by a permutation approach of randomly reallocated vs. non-reallocated data. See 'Details'.
Function multirunge [nlsrk v1.1]
keywords
nonlinear
title
Runge-Kutta numerical solver (single point, multivariate)
description
Solves numerically an initial conditions problem for a set of Ordinary Differential Equations (ODE) by Runge-Kutta 4 method. Integrates numerically the equations from tmin to tmax by steps of dt.
Function nlscontour [nlsrk v1.1]
keywords
nonlinear
title
Contour plot for nonlinear least squares
description
Takes as central values the results of non-linear least square fitting by the nls(base, stats) function, then draws a contour plot of the residual sum of squares function around these values.