safe.toptable

safe

 Number of categories to be printed. If omitted, the first 10 categories are reported. 

number

 Logical determining whether p-values smaller than 10^-4 are output in scientific notation, rather than as decimals. By default <code>pretty = TRUE</code>. 

pretty

 Logical determining whether category descriptions are appended to printed output. By default <code>description = TRUE</code>. 

description


  Prints annotated results from <code>SAFE</code> 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.


 htest

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

William T Barry

Significance Analysis of Function and Expression

safe.toptable function

Number of categories to be printed. If omitted, the first 10 categories are reported.

Logical determining whether p-values smaller than 10^-4 are output in scientific notation, rather than as decimals. By default <code>pretty = TRUE</code>.

Logical determining whether category descriptions are appended to printed output. By default <code>description = TRUE</code>.

Prints annotated results from <code>SAFE</code> 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.

safe.toptable: Category-specific results from SAFE

Description

Usage

Arguments

References

See Also