report: Generate report for CePa analysis

Description

Generate report for CePa analysis

Usage

report(x, adj.method = "none", cutoff = ifelse(adj.method == "none", 0.01, 0.05),
    template.file = system.file(package = "CePa", "extdata", "cepa.template"),
    only.sig = TRUE, dir.path = NULL, ...)

Arguments

x: a cepa.all object
adj.method: methods in p.adjust, available methods are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
cutoff: cutoff for significance
template.file: path of the template file
only.sig: whether to generate detailed report for every pathway. If it is set to FALSE, the page for every pathway under every centrality would be generated (there would be so many images!).
dir.path: dir name
...: other arguments

Author

Zuguang Gu <z.gu@dkfz.de>

Details

The report is in HTML format that you can view it in you web browser. Networks for pathways can be visualized interactively (by using Cytoscape Web, in which you can drag the network, zoom in and zoom out the network). To load Flash Player successful in you browser, you may need to set the Flash security settings on your machine.

The report would locate at the current working directory. View the report by clicking index.html in the report directory.

There is also another popular method qvalue to adjust p-values. Turn to plot.cepa.all to find out how to use qvalue.

Examples

Run this code

if (FALSE) {
data(PID.db)

# ORA extension
data(gene.list)
# will spend about 20 min
res.ora = cepa.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI)
report(res.ora)
}