circle_dat: Creates a plotting object.

Description Usage Arguments Details Examples

View source: R/GOCore.R

Description

The function takes the results from a functional analysis (for example DAVID) and combines it with a list of selected genes and their logFC. The resulting data frame can be used as an input for various ploting functions.

Usage

1
circle_dat(terms, genes)

Arguments

terms

A data frame with columns for 'category', 'ID', 'term', adjusted p-value ('adj_pval') and 'genes'

genes

A data frame with columns for 'ID', 'logFC'

Details

Since most of the gene- annotation enrichment analysis are based on the gene ontology database the package was build with this structure in mind, but is not restricted to it. Gene ontology is structured as an acyclic graph and it provides terms covering different areas. These terms are grouped into three independent categories: BP (biological process), CC (cellular component) or MF (molecular function).

The "ID" and "term" columns of the terms data frame refer to the ID and term description, whereas the ID is optional.

The "ID" column of the genes data frame can contain any unique identifier. Nevertheless, the identifier has to be the same as in "genes" from terms.

Examples

1
2
3
4
5
6
7
8
## Not run: 
#Load the included dataset
data(EC)

#Building the circ object
circ<-circular_dat(EC$david, EC$genelist)

## End(Not run)

GOplot documentation built on May 29, 2017, 11:17 p.m.