gene.results: Gene-specific results from SAFE
In safe: Significance Analysis of Function and Expression

Description Usage Arguments Author(s) References See Also

Provides gene-specific local statistics and resampling-based p-values for every feature in the category of interest. Features are ordered by the degree and direction of differential expression.

1 2	gene.results(object, cat.name = NULL, error = "none", print.it = TRUE, gene.names = NULL)

`object`	Object of class `SAFE`.
`cat.name`	Name of the category to be displayed. If omitted, the most significant category is displayed.
`error`	Specifies a non-resampling based method for adjusting the empirical p-values. A Bonferroni, ("FWER.Bonf"), Holm's step-up ("FWER.Holm"), and Benjamini-Hochberg step down ("FDR.BH") adjustment can be selected. By default ("none") no error rates are computed.
`print.it`	Logical determining whether results are printed to screen or returned as a list of data.frames for up- and down-regulated genes.
`gene.names`	Optional character vector of gene names to append to the SAFE output.

William T. Barry: bbarry@jimmy.harvard.edu

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.

safe.

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