gene.results {safe} | R Documentation |
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.
gene.results(object = NULL, cat.name = NULL, error = "none", print.it = TRUE)
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. |
William T. Barry: bill.barry@duke.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, Bioinformatics {bf 21}(9) 1943–1949.
See also the vignette included with this package.
{safe
.}