gene.results {safe}R Documentation

Gene-specific results from SAFE

Description

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

Usage

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

Arguments

object Object of class SAFE.
cat.name Name of the category to be plotted. If omitted, the most significant category is plotted.
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 results for up- and down-regulated genes.

Author(s)

William T. Barry: bill.barry@duke.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, Bioinformatics {bf 21}(9) 1943–1949.

See also the vignette included with this package.

See Also

{safe.}


[Package safe version 2.2.0 Index]