Package 'malani'

A matrix of expression values.

Description

A numeric matrix 100*20.

Usage

dat

Format

matrix.

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A vector of class labels for dat.

Description

Vector length of 20.

Usage

grp

Format

vector

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G SVM models.

Description

Returns accuracy performance of all genes. G support vector machine (SVM) classifiers trained using G different data matrixes, are used to predict labels in test data. Models are ranked based on prediction performances.

Usage

Gsvmod(dat.train, lab.train, dat.test, lab.test)

Arguments

dat.train	Train data with G features and (k-1)*S/k samples. Parameter k comes from cross-validation scheme and is specified by user (default is 2).
lab.train	Class labels for train data.
dat.test	Test data with G features and S/k samples.
lab.test	Class labels for test data.

Value

Accuracy scores for models. Each model represents one gene.

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Select initial gene list from original data matrix.

Description

Train G-1 SVM models in k-fold cross validation scheme to select initial genes list.

Usage

intGenes(dat, grp, nfolds.out = 2, top.per = 0.05)

Arguments

dat	Original gene expression data matrix with G rows (number of genes) and S column (number of samples).
grp	Class labels.
nfolds.out	Outer cross validation number (default is 2).
top.per	All genes are ranked based on their models performance and top.per% of them are selected as initial genes.

Value

Selected initial genes.

Examples

data(malanidata)
int <- intGenes(dat,grp)
print(int$top.genes)

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Dataset for malani package

Description

A numeric matrix G*S contains gene expressions data. G are the genes (rows) and S are the samples (columns).

Usage

malanidata

Format

A matrix of numeric values, 100 genes, 20 samples and class labels.

Examples

data(malanidata)

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Find best performing pairs

Description

Combine each gene in initial set with all genes in the original set. Top npair pairs are selected to construct the Q matrix.

Usage

pairmod(X, LX, theta, npair = 10)

Arguments

X	Original gene expression data matrix. With G rows (number of genes) and S column (number of samples).
LX	Class labels.
theta	Initial gene set.
npair	Given a gene in initial set, top npair best performing pairs correspond to that gene are selected (Default is 10).

Value

Best (npair*G/20) performing pairs.

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