Re: [R] Changing a for loop to a function using sapply

Sun, 21 Oct 2012 12:52:25 -0700 

Hello,
You're right an _explicit_ for loop is not necessary in your case, but note that the *apply functions are just for loops in disguise. They are also the prefered R idiom. In this case I've used ?replicate, a function of the *apply family. To be more readable it uses a new function, called iteratively. I believe that the end result looks simpler than the explicit loop version, but that's a matter of taste. 


# Changed from character vector to function
random.string <- function(n)
    rep(NA, rs <- sample(3:n, 1, replace = TRUE))

# Unchanged
randomizeString <- function(x) {
    DNAnucleotides<- c("a","c","g","t")
    a <- sample(DNAnucleotides, 3, replace = TRUE)
    return(a)
}

# Changed to use function random.string()
DNA <- character(20)
for(i in 1:20)

    DNA[i] <- paste(unlist(sapply(random.string(21), randomizeString, 
simplify = TRUE)), collapse = "")

DNA

# New function. Note the use of lapply, not sapply
fun <- function(n){
    paste(unlist(lapply(random.string(n), randomizeString)), collapse = "")
}

DNA2 <- replicate(20, fun(21))
DNA2


Hope this helps,

Rui Barradas
Em 21-10-2012 16:14, Ed escreveu:

Apparently there is one or more concepts that I do not fully 
understand from the descriptions of a function and the apply 
material.   I have been reading the mail from this forum and have 
learned much but, in this case, what I have been reading here and from 
the manual isn't enough.
The following code produces what I want with the for loop.  From what 
I have read from this forum, a for loop its not necessarily the best 
path so I tried to create a function do to the same work.


Using the following 64 bit version on Windows 7 Dell laptop
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)



below is the part that works

################################################################################ 

# The following lines create a string of nucleotides and uses a for 
loop to create multiple strings.

# random.string replicate something based on rs sampling criteria.

random.string <- rep(NA, rs<-sample(3:18,1,replace = TRUE))


# The randomizeString function uses members of DNAnucleotides list to 
sample 3 at a time

# placing the results in "a".

randomizeString <- function(x) {
    DNAnucleotides<- c("a","c","g","t")
    a <-sample(DNAnucleotides,3, replace = TRUE)
    return(a)
    }


# The following paste output uses random.string to indicate the number 
of times the function
# randomizeString selects a triplet from the list DNAnucleotides to 
create a text string

# of a sequence of nucleotides.

# collapse = "" removes the quotes from the triplets to produce one 
long string when the string

# is printed by paste.


paste(c(sapply(random.string, randomizeString, simplify = TRUE), ""), 
collapse = "")



# The for loop uses the paste output to create multiple random length 
nucleotide strings

# which can be printed to a file.


for(i in 1:20) DNA[i]<-paste(c(sapply(rep(NA, 
rs<-sample(3:21,1,replace = TRUE))

, randomizeString, simplify = TRUE), ""), collapse = "")
DNA


Rowname <- c(1:20)     # provides row numbers to be used with the 
sequences produced
Arrow<- rep(">",20)     # provides a list of ">" to be used to 
separate the row numbers and sequences



# DNAout uses a for loop to combine the vectors to create one string 
vector of sequences.


DNAout<-class(character)

for(j in 1:20)DNAout[j]<- paste(Rowname[j]," ",Arrow[j]," ",DNA[j], 
collapse = "" )

DNAout


################################################################################################ 




Here is what I have tried in attempts to create a function to 
replicate the results of the for loop above.

This one comes close.

#This repeats the above script without the comments.
######
options(stringsAsFactors=FALSE)
DNA<-class(character)
randomizeString <- function(x) {
    DNAnucleotides <- c("A","C","G","T")
    a <-sample(DNAnucleotides, 3, replace = TRUE)
    return(a)
    }

for(i in 1:20) DNA[i]<-paste(c(sapply(rep(NA, 
rs<-sample(3:18,1,replace = TRUE))

, randomizeString, simplify = TRUE), ""), collapse = "")
DNA
Rowname <- c(1:20)
Arrow<- rep(">",20)

DNAout<-class(character)

for(j in 1:20)DNAout[j]<- paste(Rowname[j]," ",Arrow[j]," ",DNA[j], 
collapse = "" )

DNAout
#######
##The following works partially
DNAoutc <- class("character")

DNAoutc <- function(x,y,z){sapply(x, paste(x," ",y," ",z,"\n", 
collapse = ""))}

DNAoutc(Rowname,Arrow,DNA)

Error in get(as.character(FUN), mode = "function", envir = envir) :
  object '1   >   ACAAACAATGAGGTCCGCCGGATGAAGCTG
2   >   CAAACCTCGTGCAAAGGTGCTTCATGGTAAATCCGTTTAGCTTTTCGGGAAAGT
3   >   TACATCGAAGCTCGTGGGGTGAAG
4   >   CGTCAACATGAACAAATGACATCCAGACGCACGCTGTAA
5   >   CATTTAACCCTTGGTGTGATG
6   >   AAGTATGAGTGGGCCTTGGGTTCTGGCTCCCACGCGTTGTGC
7   >   AGTTCCCGCAAACTGATACTGATCAGCACTTAGAGACCGCCACTATCAGTT
8   >   AATAATGCATGCTAGGCAGCCCGCTCGACCATTAGGGATAGAGCT
9   >   GACATCAAGTCATAGGTT
10   >   CAGAACAATATACACGTT
11   >   CGCAACCATCTACACTGCGTT
12   >   GTGAACTGAGGTATGACCAAAAGGTGGATAATACCCCACGGGACC
13   >   TAGCAACATGAGTGCCTCAGGTTGTCGTTCAATAAACTCGGGAAG
14   >   GCGATGATCCGCTTATAGCATGGACAAAGCAACGTTCTGTCGTCGGATTCGGGG
15   >   AGCATGTTAGCAACCCCTTTG
16   >   ACTAGTTCTGCCGTCATTTCAATG
17   >   ATTCTTCCCTTG
18   >   CATCTCGATTCTTTCTTACAATGT
19   >   ATAGATACCTTGGTCAAATAATCGTTTCAAGGT
20   >   GGGGTGGATAATAGCGGATAC
' of mode 'function' was not found
########################################

My other attempts essentially give errors which I can not seem to 
figure out what I am missing to correct the errors.

Below are a few of the failed attempts.
#####################################

mode(DNAoutf)<-("function")

DNAoutf <-  sapply(x,function(x,y,z){paste(x," ",y," ",z,"\n", 
collapse = "" )})

DNAoutf(Rowname,Arrow,DNA)

> mode(DNAoutf)<-("function")
Error in mode(DNAoutf) <- ("function") : object 'DNAoutf' not found

> DNAoutf<- function(x,y,z) {sapply(x,y,z),paste(x," ",y," ",z,"\n", 
collapse = "" ))}

Error: unexpected ',' in "DNAoutf<- function(x,y,z) {sapply(x,y,z),"
> DNAoutf(Rowname,Arrow,DNA)
Error: could not find function "DNAoutf"

#######################################
mode(DNAoutf)<-("function")

DNAoutf <-  sapply(x,function(x,y,z){paste(x," ",y," ",z,"\n", 
collapse = "" )})

DNAoutf(Rowname,Arrow,DNA)

> mode(DNAoutf)<-("function")
Error in mode(DNAoutf) <- ("function") : object 'DNAoutf' not found

> DNAoutf <-  sapply(x,function(x,y,z){paste(x," ",y," ",z,"\n", 
collapse = "" )})

Error in paste(x, " ", y, " ", z, "\n", collapse = "") :
  argument "y" is missing, with no default
> DNAoutf(Rowname,Arrow,DNA)
Error: could not find function "DNAoutf"

############################################

DNAouts(Rowname,Arrow,DNA) <- sapply(x,function(x,y,z){paste(x," ",y," 
",z,"\n", collapse = "" )})

DNAouts


> DNAouts(Rowname,Arrow,DNA) <- sapply(x,function(x,y,z){paste(x," 
",y," ",z,"\n", collapse = "" )})

Error in paste(x, " ", y, " ", z, "\n", collapse = "") :
  argument "y" is missing, with no default

##############################################
DNAouts <- class("character")

DNAouts <- sapply(x,function(Rowname,Arrow,DNA){paste(x," ",y," 
",z,"\n", collapse = "",simplify, USE.NAMES)})

DNAouts

> DNAouts
Error: object 'DNAouts' not found
> DNAouts <- class("character")

> DNAouts <- sapply(x,function(Rowname,Arrow,DNA){paste(x," ",y," 
",z,"\n", collapse = "",simplify, USE.NAMES)})
Error in paste(x, " ", y, " ", z, "\n", collapse = "", simplify, 
USE.NAMES) :

  object 'z' not found
> DNAouts
[1] "character"
>
#######################################################

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and provide commented, minimal, self-contained, reproducible code.






















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