Question

8.Write in R code.

a)stimulate a string of 10,000 characters drawn uniformly and independently for the set {A,C,G,T} [HINT: sample]

b) create a frequency table of the string [HINT:table]

c) write a function to create a contingency table of adjacent k-tuples. For example, with k=3 and with the string "CAGACAAAAC", you would want to produce the following table: [ ONLY USE FOR LOOPS AND PASTE (,collapse=""), DO NOT USE EMBED, SUBSTR, or DO.CALL]

AAA AAC ACA AGA CAA CAG GAC

2 1    1 1 1 1 1

Answer 1

Answer:

Given that :

a) stimulate a strong of 10,000 characters drawn uniformly and independently for the set{A,C,G,T}

R code with comments

#set the random seed for repeatability
set.seed(123)

#set the string
x<-c("A","C","G","T")
#set the number of simulations
R<-10000

#part a)
#simulate a string of R characters
s<-sample(x,size=R,replace=TRUE)

#part b)
#create a frequency table
table(s)

#part c
getTable<-function(y,k){
#initialize the result
result<-character(0)
#go through the string, k places at a time
for (i in 1:(length(y)-k+1)){
#get k characters and concat
result<-rbind(result,paste(y[i:(i+k-1)],collapse=""))
}
#create the contigency table
out<-table(result)
return(out)
}

#test the function given in the example
s1<-c("C","A","G","A","C","A","A","A","A","C")
getTable(s1,3)

#test the function on the string from part a)
getTable(s,3)

--------

#get this