R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 21 found.
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BetaMixture-class (Package: PANR) :

This S4 class includes methods to do beta-mixture modelling of functional gene associations given rich phenotyping screens.

● Data Source: BioConductor
● Keywords: classes
● Alias: BetaMixture, BetaMixture-class
● 0 images

PAN-class (Package: PANR) :

This S4 class includes methods to infer posterior association networks and enriched modules of functional gene interactions from rich phenotyping screens.

● Data Source: BioConductor
● Keywords: classes
● Alias: PAN, PAN-class
● 0 images

SNR2p (Package: PANR) :

The function translate Signal-to-Noise Ratios to p-values based on the fitted mixture model.

● Data Source: BioConductor
● Keywords:
● Alias: SNR2p, SNR2p,BetaMixture,numeric_Or_integer-method
● 0 images

assoScore (Package: PANR) :

This function compute similarity scores to quantify associations between pairs of genes, given measured rich phenotypes.

● Data Source: BioConductor
● Keywords:
● Alias: assoScore
● 0 images

buildPAN (Package: PANR) :

The function builds a graph for the inferred PAN so that it can be visualize in igraph or RedeR

● Data Source: BioConductor
● Keywords:
● Alias: buildPAN, buildPAN,PAN,character_Or_missing,list_Or_missing,logical_Or_missing-method
● 0 images

cosineSim (Package: PANR) :

This function compute cosine similarities or distances between pairs of genes, given measured rich phenotypes.

● Data Source: BioConductor
● Keywords:
● Alias: cosineDist, cosineSim
● 0 images

data-Bakal2007 (Package: PANR) :

The data set we use here comes from quantitative morphological screening for 249 gene-overexpression or RNAi knock-down experiments. For each individual cell, 145 different geometric features were computed by imaging analysis, and are subsequently scored with NNs trained to discriminate seven reference TCs with distinctive morphologies. For each TC, NN z-scores were computed from all scored cells in this TC (more details in Bakal 2007).

● Data Source: BioConductor
● Keywords:
● Alias: Bakal2007, Bakal2007Cluster, bm1, nodeColor
● 0 images

edgeWeight (Package: PANR) :

This is an internal function to compute edge weights before inferring a posterior association network.

● Data Source: BioConductor
● Keywords: internal
● Alias: edgeWeight, edgeWeight, PAN-method
● 0 images

exportPAN (Package: PANR) :

Powered by function write.graph in package igraph, this function writes the inferred PAN or module graphs to files in a variety of formats that are supported by igraph.

● Data Source: BioConductor
● Keywords:
● Alias: exportPAN, exportPAN,PAN,character_Or_missing,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method
● 0 images

fitBM (Package: PANR) :

The function fits a three-beta mixture model to densities of functional gene associations computed from rich phenotyping screens.

● Data Source: BioConductor
● Keywords:
● Alias: fitBM, fitBM,BetaMixture,list_Or_missing,list_Or_missing,logical_Or_missing-method
● 0 images