glmroastlist: Multiple Contrast Rotation Tests based on Marginal...
In daniel-gerhard/mcroast: Multiple Contrast Rotation Tests

Description Usage Arguments Details Value Author(s) References

Adaption of the roast function in package limma to perform a maxT-test for parameters in multiple generalized linear models, controlling FWER for multiple contrasts.

1	glmroastlist(glmlist, K, nrot = 9999, adjusted = TRUE)

`glmlist`	A list with multiple glm objects, each with the same design matrix.
`K`	A contrast matrix (different contrasts in rows), with the same number of columns as number of parameters in the model
`nrot`	Number of Monte Carlo simulation steps
`adjusted`	logical, if TRUE single-step maxT FWER control is performed; if FALSE the comparison-wise error rate is controlled

Most of the code was taken from function roast in package limma (Bioconductor).

A list with

`Y`	The matrix of response variables
`X`	The design matrix
`statistic`	A matrix of test statistics
`pvalue`	A matrix of (adjusted) p-values
`B`	A matrix with contrast parameter estimates
`mrot`	A vector with simulated maxT statistics under H0

Daniel Gerhard

Wu, D, Lim, E, Francois Vaillant, F, Asselin-Labat, M-L, Visvader, JE, and Smyth, GK (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26, 2176-2182.

Langsrud, O (2005). Rotation tests. Statistics and Computing 15, 53-60.

daniel-gerhard/mcroast documentation built on May 14, 2019, 3:38 p.m.