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iTOP (version 1.0.2)

Inferring the Topology of Omics Data

Description

Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples. We based this methodology on the RV coefficient (Robert & Escoufier, 1976, ), a measure of matrix correlation, which we have extended for partial matrix correlations and binary data (Aben et al., 2018, ).

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Version

Install

install.packages('iTOP')

Monthly Downloads

183

Version

1.0.2

License

GPL-2

Maintainer

Nanne Aben

Last Published

June 13th, 2018

Functions in iTOP (1.0.2)

run.bootstraps

Bootstrapping procedure
compute.config.matrix

Computes a configuration matrix
inner.product

Inner product similarity.
bootstrap.config.matrices

Performing a single bootstrap
rv.pcor

Determining a (partial) RV coefficient
intersect.samples

Intersect samples between datasets.
jaccard

Jaccard similarity.
rv.pval

Determining a p-value the (partial) RV coefficient
compute.config.matrices

Compute configuration matrices
rv.coef

Computes the RV coefficient
rv.conf.interval

Determining a confidence interval for the (partial) RV coefficient
permute.config.matrices

Performing a permutation
rv.link.significance

Wrapper function to determine significance in the PC algorithm
process.custom.config.matrix

Process a custom configuration matrix.
rv.cor.matrix

A correlation matrix of RV coefficients
run.permutations

Permutations for significance testing