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Perform cross-validation for the function that implements the "sparse Poisson linear discriminant analysis classifier", which is similar to linear discriminant analysis but assumes a Poisson model rather than a Gaussian model for the data. The classifier soft-thresholds the estimated effect of each feature in order to achieve sparsity. This cross-validation function selects the proper value of the tuning parameter that controls the level of soft-thresholding.
● Data Source:
CranContrib
● Keywords:
● Alias: Classify.cv
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This function computes a Poisson dissimilarity matrix as described in the paper referenced below, and is intended to be applied to a data matrix of counts resulting from a sequencing experiment. The (i,k) element of the Poisson dissimilarity matrix is the dissimilarity between observations i and k of the data matrix x: that is, the log likelihood ratio statistic under a simple Poisson model.
● Data Source:
CranContrib
● Keywords:
● Alias: PoissonDistance
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Classify observations using a simple Poisson model. This function implements the "sparse Poisson linear discriminant analysis classifier", which is similar to linear discriminant analysis but assumes a Poisson model rather than a Gaussian model for the data. The classifier soft-thresholds the estimated effect of each feature in order to achieve sparsity.
● Data Source:
CranContrib
● Keywords:
● Alias: Classify
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A simple approach for performing classification and clustering of samples for which RNA sequencing data is available. Based upon a simple Poisson model proposed by a number of authors (e.g. Marioni et al Genome Research 2008, Bullard et al BMC Bioinformatics 2010, and others).
● Data Source:
CranContrib
● Keywords:
● Alias: PoiClaClu, PoiClaClu-package
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ColorDendrogram
(Package: PoiClaClu) :
Color the leaves in a hierarchical clustering dendrogram
Pass in the output of "hclust" and a class label for each observation. A colored dendrogram will result, with the leaf colors indicating the classes.
● Data Source:
CranContrib
● Keywords:
● Alias: ColorDendrogram
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1 images
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Find a constant alpha, 0<alpha<=1, such that x raised to the power alpha approximately follows the simple Poisson log linear model that says that the (i,j) element of x is Poisson with mean si times gj, where si is a sample-specific term and gj is a feature-specific term. Alpha is selected via a grid search.
● Data Source:
CranContrib
● Keywords:
● Alias: FindBestTransform
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Internal PoiClaClu functions
● Data Source:
CranContrib
● Keywords: internal
● Alias: NullModel, NullModelTest, print.poicla, print.poiclacv, print.poidist
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Generate two nxp data sets: a training set and a test set, as well as outcome vectors y and yte of length n indicating the class labels of the training and test observations.
● Data Source:
CranContrib
● Keywords:
● Alias: CountDataSet
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providing 
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