go.profiles: GO enrichment comparison

In ProNet: Biological Network Construction, Visualization and Analyses

Description

GO enrichment comparison between networks.

Usage

go.profiles(g_ref, g_comp, color = c("red", "white"), onto = c("MF", "BP",
  "CC"), mode = c("number", "frequency"), demonstration.number = 10,
  plot = TRUE, ...)

Arguments

g_ref	Vector of the first set of molecules.
g_comp	Vector of the second set of molecules.
color	Color represent of the two sets.
onto	GO categories, three possible values are MF for GO function, BP for GO process, and CC for GO componet
mode	Mode of the GO vlues, either Frequency or Number.
demonstration.number	Number of the top GOs to display.
plot	Logical value, whether to plot the profiling result (if TRUE) or not (if FALSE).
...	other arguments.

Value

A data frame of the profiling result and plots.

Examples

entrez1<-c("11067","414157","196477","147339","642")
entrez2<-c("121549","51160","83878","11338","196477","9319","608","7015")
go.profiles(entrez1,onto="MF",main="Only Network 1")
go.profiles(entrez1,entrez2,onto="MF",main=c("Network 1 vs 2"))

Example output

Loading required package: Rcpp
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: MCL
Loading required package: linkcomm
Loading required package: RColorBrewer

Welcome to linkcomm version 1.0-11

For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))

                               GO_term       GOID entrez1
1                      protein binding GO:0005515       2
2              aminopeptidase activity GO:0004177       1
3            carboxypeptidase activity GO:0004180       1
4 cysteine-type endopeptidase activity GO:0004197       1
5                   peptidase activity GO:0008233       1
6     cysteine-type peptidase activity GO:0008234       1
                                GO_term       GOID entrez1 entrez2
1                       protein binding GO:0005515       2       6
2               aminopeptidase activity GO:0004177       1       0
3             carboxypeptidase activity GO:0004180       1       0
4  cysteine-type endopeptidase activity GO:0004197       1       0
5                    peptidase activity GO:0008233       1       0
6      cysteine-type peptidase activity GO:0008234       1       0
7                    nucleotide binding GO:0000166       0       2
8                           DNA binding GO:0003677       0       2
9       transcription cofactor activity GO:0003712       0       1
10                  telomerase activity GO:0003720       0       1

ProNet documentation built on May 30, 2017, 2:02 a.m.