Gene-specific results from SAFE

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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

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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: bbarry@jimmy.harvard.edu

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.