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.
