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.
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.
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.