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

Ed beary at geneseo.edu
Sun Oct 21 17:14:33 CEST 2012

```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
########################################
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")
> 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")
> 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
> 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) :