Question

I have 507 tables with (pattern = “human”).
Inside each table there are a number of columns that I want to compare via Student’s t-test. Before I learned ‘functions’, I was initializing 16 columns in my data.frame and copying a lot of code for 16 comparisons. 🙁 But I want to simplfy the code by using functions.

Q: Do I need a counter of some sort or to use ‘cbind’? or what??
Any suggestions?

files_to_test <- list.files(pattern="human")  
num_files <- length(files_to_test)  

## Function: Calculate t-test P-values ##
g<-function(compareA,compareB) {
   for (i in 1:num_files){
      temp <- read.table(files_to_test[i], header=TRUE, sep="\t")
      ## Obtain Columns To Compare ##
      colA <- temp[compareA]
      colB <- temp[compareB]
      ttr <- t.test(colA, colB, var.equal=TRUE)
      tt_pvalues[i,1] <- ttr$p.value
      }
tag <- paste(compareA, compareB, sep="_Vs_")
tt_titles <- data.frame(tag,tt_titles) # Here is my problem.  
ALL_pvalues <- data.frame(tt_pvalues, ALL_pvalues) # Here is my problem.  
}

## Comparison 1
compareA <-"log_b" 
compareB <-"log_b_rich"
g(compareA,compareB)

## Comparison 2
compareA <-"fc_Etoh_CDT_tot_poly"
compareB <-"log_b_rich"
g(compareA,compareB)

My expected output should be:

source.file.name, tag[i], tag[j], ...  
files_to_test[1], #, #, ...  
files_to_test[2], #, #, ...  

What I am trying to do is append or fold my newly tabulated ttest data with the earlier ttest data, either by cbind or data.frame. I’m not sure.

Answer 1

I think you need to move the tagging operation inside the loop:

# Pre-allocate tag[i] outside the loop
tag <- vector("character", length=num.files)

g<-function(compareA,compareB) {
   for (i in 1:num_files){
      temp <- read.table(files_to_test[i], header=TRUE, sep="\t")
      ## Obtain Columns To Compare ##
      colA <- temp[compareA]
      colB <- temp[compareB]
      ttr <- t.test(colA, colB, var.equal=TRUE)
      tt_pvalues[i,1] <- ttr$p.value
   tag[i] <- paste(compareA, i, "Vs" compareB, i sep="_")
      }

tt_titles <- data.frame(tag, tt_titles) # Here is my problem.  
ALL_pvalues <- data.frame(tt_pvalues, ALL_pvalues) # Here is my problem.  
}