internal: Internal functions

In globalSeq: Global Test for Counts

Description

This page lists and describes all internal functions of the R package globalSeq.

Preparation
intern.estim estimates the parameters of the negative binomial distribution by maximum likelihood.
intern.permu permutes values across samples, either across all samples or across samples within subgroups.
intern.score computes the score test statistic.

Testing
intern.crude calculates p-values by permutation.
intern.focus calculates p-values by permutation, focusing on a region of interest.
intern.conva calculates p-values by permutation, using the method of control variates.

Decomposition
intern.cov decomposes the test statistic to show the influence of covariates.
intern.sam decomposes the test statistic to show the influence of samples.
intern.plot plots the contributions of covariates or samples.

Communication
intern.chromo runs through all genes on a chromosome.
intern.select identifies local covariates.
intern.matrix transforms data to a numeric matrix.

See Also

The user functions of the R package globalSeq are cursus, omnibus and proprius.

globalSeq documentation built on Nov. 8, 2020, 7:22 p.m.