PLEASE DO NOT POST IN HTML:
On Dec 14, 2014, at 12:30 PM, Kruti Pandya kp1...@gmail.com wrote:
I am new to R and using this package BoolNet. I wanted to extract the
boolean transition functions resulting from the output of
generateRandomNKNetwork function. I am able to extract individual function
using
net$interactions$Gene1$expression,net$interactions$Gene2$expression .
But it gives me the transition function in quotes. How can I remove the
quotes ?
My goal is to evaluate each transition function at a randomly generated
initial state. What I need to do is to extract each of the individual
functions one by one. Like
extract net$interactions$Gene1$expression
evaluate the function at random initial sate
then extract net$interactions$Gene2$expression
evaluate the function at random initial state
do this for all five functions that comes out of the ouput.
I tried something like this but did not work.
for (i in 1:5){
func[[i]]-rn$interactions$Gene[i]$expression
#extract net$interactions$Gene1$expression,
net$interactions$Gene2$expression and so on
}
So look at the object:
str(net)
List of 3
$ genes : chr [1:5] Gene1 Gene2 Gene3 Gene4 ...
$ interactions:List of 5
..$ Gene1:List of 3
.. ..$ input : int [1:3] 5 4 3
names(net$interactions)
[1] Gene1 Gene2 Gene3 Gene4 Gene5
There are not five items names named “Gene” with indices 1 to 5. You can get at
items with those names by paste0()-ing with “[[“
#There is nothing named “fun” yet:
OR FOR THAT MATTER…. an object name “rn”. Why on earth did you change the name
to 'rn' from ‘net'?
func=list()
for (i in 1:5){
func[[i]]-net$interactions[[paste0(Gene,i)]]$expression
}
str(func)
List of 5
$ : chr (!Gene5 !Gene4 !Gene3) | (!Gene5 !Gene4 Gene3) | (Gene5
!Gene4 Gene3) | (Gene5 Gene4 Gene3)
$ : chr (!Gene1 Gene2 !Gene3) | (!Gene1 Gene2 Gene3) | (Gene1
!Gene2 !Gene3) | (Gene1 !Gene2 Gene3) | (Gene1 Gene2 | __truncated__
$ : chr (!Gene4 !Gene2 Gene5) | (Gene4 Gene2 !Gene5) | (Gene4 Gene2
Gene5)
$ : chr (!Gene1 !Gene2 Gene5) | (!Gene1 Gene2 Gene5) | (Gene1
!Gene2 Gene5) | (Gene1 Gene2 !Gene5)
$ : chr (!Gene5 !Gene1 !Gene4) | (!Gene5 Gene1 !Gene4) | (!Gene5
Gene1 Gene4) | (Gene5 !Gene1 !Gene4) | (Gene5 !Gene1| __truncated__
David.
# output of generateRandomNKNetwork
install.packages(BoolNet)
library(BoolNet)
net-generateRandomNKNetwork(5,3,readableFunctions=canonical)
#Output of net
Boolean network with 5 genes
Involved genes:
Gene1 Gene2 Gene3 Gene4 Gene5
Transition functions:
Gene1 = (!Gene5 Gene1 !Gene2) | (!Gene5 Gene1 Gene2) | (Gene5
!Gene1 !Gene2)
Gene2 = (!Gene1 !Gene3 !Gene2) | (!Gene1 Gene3 !Gene2) | (!Gene1
Gene3 Gene2) | (Gene1 Gene3 Gene2)
Gene3 = (!Gene3 Gene1 !Gene2) | (Gene3 !Gene1 !Gene2) | (Gene3
Gene1 !Gene2)
Gene4 = (!Gene4 !Gene2 !Gene1) | (!Gene4 !Gene2 Gene1) | (!Gene4
Gene2 Gene1) | (Gene4 !Gene2 !Gene1) | (Gene4 Gene2 Gene1)
Gene5 = (!Gene2 !Gene4 !Gene5) | (!Gene2 !Gene4 Gene5) | (Gene2
!Gene4 Gene5)
net$interactions$Gene1$expression
#[1] (!Gene5 Gene1 !Gene2) | (!Gene5 Gene1 Gene2) | (Gene5
!Gene1 !Gene2)
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Alameda, CA, USA
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
