creation of a dataframe in for cycle

[eleme96]

Hi, I need help about the creation of a dataframe where for every for cycle I have to add a new column in dataframe with the new values.

Here's the content of the network (called rf.txt in the code)

targets	,	factors
BDNF,           BDNF
SEM3A,          SEM3A
TALIN,          BDNF
VINCULIN,       BDNF
ALFAACTININ,    BDNF
FAK	,	TALIN 
DOCK180	,	FAK
GRAF	,	FAK
CDC42	,	DOCK180
RAC1	,	DOCK180 | PIX
PAK2_3	,	CDC42 | RAC1
PIX	,	PAK2_3
GIT	,	PIX
PXN	,BDNF &!GIT
RHOA	,	SEM3A &! GRAF
NWASP	,	CDC42
WAVE	,	RAC1
SSH	,	RAC1
ROCK	,	RHOA
MLCK    , MLCK   &!PAK2_3
MLCP, MLCP &! ROCK
MLC_P	,	ROCK | MLCK &!MLCP
LIMK	,	PAK2_3
ADFCOFILIN ,SSH &!LIMK
ARP2_3	,	NWASP | WAVE
RF	,	MLC_P | ADFCOFILIN
PROTR	,	ARP2_3 &! RF

This is the code:

library(BoolNet)
setwd("C:/Users/eleme/OneDrive/Desktop/tesi")
a=loadNetwork("rf.txt")
#print(a)
list= generateState(a,specs=c("BDNF"=1,"SEM3A"=1))
#attr= getAttractors(a,type="synchronous",method = "chosen",startStates = list(list))
#print(attr)
#plot=plotAttractors(attr,title="PLOT EXHAUSTIVE SYNCHRONOUS BDNF ON",mode="table",allInOnePlot = T)


control = 0
inprob= c(0,0,0.04,0.04,0.04,0.04,
          0.04,0.04,0.04,0.04,0.04,0.04,
          0.04,0.04,0.04,0.04,0.04,0.04,
          0.04,0.04,0.04,0.04,0.04,0.04,
          0.04,0.04,0.04)

for (i in 1:10000) {
  if (i==1){
    stat1= stateTransition(a,list,type="asynchronous",
                           geneProbabilities = inprob)
    stat1=data.frame(stat1)
  }
  
  if (i!= 1){
    last_stat= stat1$stat1
    
    stat1= stateTransition(a,last_stat,type="asynchronous",
                                     geneProbabilities = inprob)
    stat1=data.frame(stat1)
   
    if (identical(stat1$stat1,last_stat)){
      control= control +1
      
    }
    else{
      control=0
    }
    
  }

  if (control==40){
    break
  }
 # print("ok")
  
  new= cbind(stat1,last_stat)
  write.table(new,file="new.csv",sep=";", append= TRUE )
  
  }

[technocrat]

The first block of code does nothing helpful here because it does not expose the data being used. a reprex. See the FAQ. So the problem can only be addressed generically.

As I understand the problem, it is to begin with a vector of values, x, and then derive through some function f a new vector, y, which will be recycled as x to f to derive a new vector y with the goal of making a data .frame object d with columns composed of x_1 \dots x_{10000}.

1. Write f for the case of one vector
2. Create a receiver object d of dimensions equal to the planned result, with the first column consisting of x_1 and the remaining columns set to NA.
3. Find a function f' to apply f successively to populate d

Candidates for f' are the apply family, it's {purrr} implementations which may or may not seem more user-friendly, and for1. It might call f recursively. One possible form for f` is

sapply(2:1e4,f)

[eleme96]

@technocrat , thanks for your answer. I haven't a good knowledge of R programming , I think I have to do this in easier way for my thesis in Biotechnology . The only thing I need to know is how to tell the program to do another column for every stat1 values ( I don't know which values and how much stat1 the for cycle creates).
The output at the moment is a simple column with many stat1 as shown in the figure attached.

[technocrat]

The screenshot appears to be a spreadsheet screenshot with a single column of character strings. This needs to be exported as a csv file for remediation before proceeding or importing directly using one of the libraries that can read whatever format the spreadsheet is. Once that is accomplished, use

dput(your_object)

and copy/paste the output into this thread. (A screenshot is useless for this purpose.)

Then we can discuss splitting out the real data from the strings.

[eleme96]

 dput(stat1)
structure(list(stat1 = c(1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), class = "data.frame", row.names = c("BDNF", 
"SEM3A", "TALIN", "VINCULIN", "ALFAACTININ", "FAK", "DOCK180", 
"GRAF", "CDC42", "RAC1", "PAK2_3", "PIX", "GIT", "PXN", "RHOA", 
"NWASP", "WAVE", "SSH", "ROCK", "MLCK", "MLCP", "MLC_P", "LIMK", 
"ADFCOFILIN", "ARP2_3", "RF", "PROTR"))`

[technocrat]

OK, thanks.

What this produces is a data frame with one column typeof numeric, but let's back up.

[quote="eleme96, post:1, topic:157384"]

a=loadNetwork("rf.txt")

[/quote]'

What a should look like but with your data from rf.txt

> print(net)
Boolean network with 4 genes

Involved genes:
Gene1 Gene2 Gene3 Gene4

Transition functions:
Gene1 = !Gene2 | !Gene3
Gene2 = Gene3 & Gene4
Gene3 = Gene2 & !Gene1
Gene4 = 1> print(net)
Boolean network with 4 genes

Involved genes:
Gene1 Gene2 Gene3 Gene4

Transition functions:
Gene1 = !Gene2 | !Gene3
Gene2 = Gene3 & Gene4
Gene3 = Gene2 & !Gene1
Gene4 = 1

Knocked-out and over-expressed genes:
Gene4 = 1
Knocked-out and over-expressed genes:
Gene4 = 1

@eleme96

list= generateState(a,specs=c("BDNF"=1,"SEM3A"=1))

Avoid naming objects with names like list which are built-in functions. What generateState returns looks like is your d put as a named vector

      BDNF       SEM3A       TALIN    VINCULIN ALFAACTININ 
          1           1           0           1           0 
        FAK     DOCK180        GRAF       CDC42        RAC1 
          0           0           0           0           0 
     PAK2_3         PIX         GIT         PXN        RHOA 
          0           0           0           0           0 
      NWASP        WAVE         SSH        ROCK        MLCK 
          0           0           0           0           0 
       MLCP       MLC_P        LIMK  ADFCOFILIN      ARP2_3 
          0           0           0           0           0 
         RF       PROTR 
          0           0 

But when we get here

@eleme96

stateTransition(a,list,type="asynchronous",

we're stuck again for lack of the original

@eleme96

a=loadNetwork("rf.txt")