report: Generate report for CePa analysis

In jokergoo/CePa: Centrality-Based Pathway Enrichment

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

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. See https://cytoscapeweb.cytoscape.org/tutorial and change the settings via https://www.macromedia.com/support/documentation/en/flashplayer/help/settings_manager04.html .

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.

Source

https://cytoscapeweb.cytoscape.org/

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa.all

Examples

## Not run: 
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)

## End(Not run)

jokergoo/CePa documentation built on July 2, 2021, 10:28 p.m.