gene.results: Gene-specific results from SAFE

In lgeistlinger/safe: Significance Analysis of Function and Expression

Gene-specific results from SAFE

Description

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.

Usage

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

Arguments

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.

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.

lgeistlinger/safe documentation built on Aug. 4, 2023, 7:34 p.m.