safe.toptable: Category-specific results from SAFE

In safe: Significance Analysis of Function and Expression

Description

Prints annotated results from SAFE as a data.frame for categories with the strongest association to response/phenotype. This includes (a) category name; (b) category size; (c) global statistic; (d) nominal empirical p-values; (e) adjusted p-values; and (f) descriptions if available.

Usage

safe.toptable(safe, number = 10, 
              pretty = TRUE, description = TRUE)

Arguments

safe	Object of class SAFE.
number	Number of categories to be printed. If omitted, the first 10 categories are reported.
pretty	Logical determining whether p-values smaller than 10^-4 are output in scientific notation, rather than as decimals. By default pretty = TRUE.
description	Logical determining whether category descriptions are appended to printed output. By default description = TRUE.

Author(s)

William T. Barry: [e-mail]

References

W. T. Barry, A. B. Nobel and F.A. Wright, 2005, Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics21(9) 1943–1949.

See also the vignette included with this package.

See Also

safe.

safe documentation built on Nov. 8, 2020, 5:37 p.m.