Conditional branching and looping in R answers

These exercises cover the sections of Conditions and Loops in R Introduction to R.

– Calculate the factorial (factorial of 3 = 3 * 2 * 1) of 10 using a loop.

for(x in 1:10){
  if(x == 1){
    factorialAnswer <- 1
  }else{
    factorialAnswer <- factorialAnswer * x 
  }
}
factorialAnswer

## [1] 3628800

– Adjusting your answer from before, what is the first number that has a factorial greater than 1000.

factorialAnswer <- 0
count <- 0

while(factorialAnswer <= 1000){
  count <- count+1
  if(count == 1){
    factorialAnswer <- 1
  }else{
    factorialAnswer <- factorialAnswer * count 
  }
}
count

## [1] 7

– Using an ifelse() expression, create a factor from a vector of 1 to 40 where all numbers less than 10 are “small”,10 to 30 are “mid”,31 to 40 are “big”

condExercise <- 1:40
condExercise

##  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
## [24] 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

vectorResult <- ifelse(condExercise<10,"small",ifelse(condExercise < 31,"mid","big"))
temp <- factor(vectorResult,levels=c("small","mid","big"),order=T)
temp

##  [1] small small small small small small small small small mid   mid  
## [12] mid   mid   mid   mid   mid   mid   mid   mid   mid   mid   mid  
## [23] mid   mid   mid   mid   mid   mid   mid   mid   big   big   big  
## [34] big   big   big   big   big   big   big  
## Levels: small < mid < big

– Read in all files from expression directory with .txt extension and create a table of gene expression results.

filesToRead <- dir("../ExpressionResults/",pattern = "*\\.txt",full.names=T)
fileRead <- vector("list",length=length(filesToRead))
for(i in 1:length(filesToRead)){
  fileRead[[i]] <- read.delim(filesToRead[i],header=F,sep="\t")
  colnames(fileRead[[i]]) <- c("GeneNames",basename(filesToRead[i]))
}
mergedTable <- NULL
for(i in fileRead){
  if(is.null(mergedTable)){
    mergedTable <- i
  }else{
    mergedTable <- merge(mergedTable,i,by=1,all=T)
  }
  
  print(nrow(mergedTable))
}

## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000
## [1] 2000

mergedTable[1:3,] 

##   GeneNames ExpressionResults_Sample1.txt ExpressionResults_Sample10.txt
## 1    Gene_1                      3.448466                       7.665488
## 2   Gene_10                      5.314180                       7.813501
## 3  Gene_100                      5.591612                       5.186500
##   ExpressionResults_Sample2.txt ExpressionResults_Sample3.txt
## 1                      5.250063                      5.968927
## 2                      5.361170                      5.305980
## 3                      6.840497                      5.197710
##   ExpressionResults_Sample4.txt ExpressionResults_Sample5.txt
## 1                      6.868251                      5.367100
## 2                      6.742855                      5.957786
## 3                      5.922931                      6.813154
##   ExpressionResults_Sample6.txt ExpressionResults_Sample7.txt
## 1                      5.189686                      3.882930
## 2                      6.293098                      7.361497
## 3                      6.228178                      5.831575
##   ExpressionResults_Sample8.txt ExpressionResults_Sample9.txt
## 1                      5.329258                      6.167451
## 2                      6.649428                      6.213910
## 3                      6.653152                      3.992555

– Add annotation from Annotation.txt. How do the pathway information for genes compare between expression table and annotation table.

Annotation <- read.table("../ExpressionResults/Annotation.ann",sep="\t",h=T)
annotatedExpression <- merge(Annotation,mergedTable,by=1,all.x=F,all.y=T)
annotatedExpression[1:2,]

##   GeneName   Ensembl     Pathway ExpressionResults_Sample1.txt
## 1   Gene_1  Ens_1001 DNA_Binding                      3.448466
## 2  Gene_10 Ens_10010 DNA_Binding                      5.314180
##   ExpressionResults_Sample10.txt ExpressionResults_Sample2.txt
## 1                       7.665488                      5.250063
## 2                       7.813501                      5.361170
##   ExpressionResults_Sample3.txt ExpressionResults_Sample4.txt
## 1                      5.968927                      6.868251
## 2                      5.305980                      6.742855
##   ExpressionResults_Sample5.txt ExpressionResults_Sample6.txt
## 1                      5.367100                      5.189686
## 2                      5.957786                      6.293098
##   ExpressionResults_Sample7.txt ExpressionResults_Sample8.txt
## 1                      3.882930                      5.329258
## 2                      7.361497                      6.649428
##   ExpressionResults_Sample9.txt
## 1                      6.167451
## 2                      6.213910

summary(annotatedExpression$Pathway)

##  DNA_Binding   Glycolysis         TGFb WntSignaling 
##         1000          500          300          200

summary(Annotation$Pathway)

##  DNA_Binding   Glycolysis         TGFb WntSignaling         NA's 
##         1000          500          300          200         3000