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Function enricher_internal [DOSE v2.10.6]
keywords
manip
title
enrich.internal
description
interal method for enrichment analysis
Function enrichDO [DOSE v2.10.6]
keywords
manip
title
DO Enrichment Analysis
description
Given a vector of genes, this function will return the enrichment DO categories with FDR control.
Function gseDO [DOSE v2.10.6]
keywords
manip
title
DO Gene Set Enrichment Analysis
description
perform gsea analysis
Function gseNCG [DOSE v2.10.6]
keywords
manip
title
NCG Gene Set Enrichment Analysis
description
perform gsea analysis
Function TransfTra [FuzzyStatTra v1.0]
keywords
manip
title
description
This function transforms a matrix of dimension n x 4 containing n trapezoidal fuzzy numbers characterized by their four values inf0,inf1,sup1,sup0 into an array of dimension nl x 3 x n containing these n fuzzy numbers characterized by means of nl equidistant \(\alpha\)-levels each (by default nl=101). The function first checks if the input matrix F is given in the correct form (tested by checkingTra). In case yes, the function returns an array given in the format explained in the function checking.
Function initialize_weightvector [ForeCA v0.2.4]
keywords
manip
title
Initialize weightvector for iterative ForeCA algorithms
description
initialize_weightvector returns a unit norm (in $\ell^2$) vector $\mathbf{w}_0 \in R^K$ that can be used as the starting point for any iterative ForeCA algorithm, e.g., foreca.EM.one_weightvector. Several quickly computable heuristics are available via the method argument.
Function get_output [LambertW v0.6.4]
keywords
manip
title
Transform input X to output Y
description
get_output transforms the input $\boldsymbol x$ to the observed data $\boldsymbol y$ given the transformation vector $\tau = (\mu_x(\boldsymbol \beta), \sigma_x(\boldsymbol \beta), \gamma, \alpha, \delta)$. This is the inverse of get_input.
Function get_input [LambertW v0.6.4]
keywords
manip
title
Back-transform Y to X
description
get_input back-transforms the observed data $\boldsymbol y$ to the (approximate) input data $\boldsymbol x_{\tau}$ using the transformation vector $\tau = (\mu_x(\boldsymbol \beta), \sigma_x(\boldsymbol \beta), \gamma, \alpha, \delta)$. Note that get.input should be deprecated; however, since it was explicitly referenced in Goerg (2011) I keep it here for future reference. New code should use get_input exclusively.
Function compute_margin_coordinates [LICORS v0.2.0]
keywords
manip
title
Get LC configuration from a (N+1)D field
description
compute_margin_coordinates computes the coordinates (boundary) of the margin of the field.
Function compute_LC_coordinates [LICORS v0.2.0]
keywords
manip
title
Computes coordinates of PLC and FLC relative to origin
description
Computes the space-time coordinates of PLC and FLC given control settings relative to the origin $(\mathbf{r}, t) = (\boldsymbol 0, 0)$. Since these coordinates do not change for different space-time positions, they can be computed once before getting the LC configurations for the entire field and then used in each call by array maskexing in get_LC_config.