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

[Rui Barradas]

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"
> >
> #######################################################
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.