Description Usage Arguments Value Examples
GO enrichment comparison between networks.
1 2 3 |
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 |
mode |
Mode of the GO vlues, either |
demonstration.number |
Number of the top GOs to display. |
plot |
Logical value, whether to plot the profiling result (if |
... |
other arguments. |
A data frame of the profiling result and plots.
1 2 3 4 | 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"))
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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
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