CODEWITHSUNDEEP
r
Ram
Ram

Reputation: 331

Evaluating dataframe and storing the result

My dataframe(m*n) has few hundreds of columns, i need to compare each column with all other columns (contingency table) and perform chisq test and save the results for each column in different variable.

Its working for one column at a time like,

s <- function(x) {
  a <- table(x,data[,1])
  b <- chisq.test(a)
}
c1 <- apply(data,2,s)

The results are stored in c1 for column 1, but how will I loop this over all columns and save result for each column for further analysis?

Upvotes: 1

Views: 401

Answers (2)

Joris Meys
Joris Meys

Reputation: 108543

If you're sure you want to do this (I wouldn't, thinking about the multitesting problem), work with lists :

Data <- data.frame(
    x=sample(letters[1:3],20,TRUE),
    y=sample(letters[1:3],20,TRUE),
    z=sample(letters[1:3],20,TRUE)
  )

# Make a nice list of indices
ids <- combn(names(Data),2,simplify=FALSE)

# use the appropriate apply
my.results <- lapply(ids,
      function(z) chisq.test(table(Data[,z]))
    )
# use some paste voodoo to give the results the names of the column indices
names(my.results) <- sapply(ids,paste,collapse="-")

# select all values for y :
my.results[grep("y",names(my.results))]

Not harder than that. As I show you in the last line, you can easily get all tests for a specific column, so there is no need to make a list for each column. That just takes longer and takes more space, but gives the same information. You can write a small convenience function to extract the data you need :

extract <- function(col,l){
    l[grep(col,names(l))]
}
extract("^y$",my.results)

Which makes you can even loop over different column names of your dataframe and get a list of lists returned :

lapply(names(Data),extract,my.results)

I strongly suggest you get yourself acquainted with working with lists, they're one of the most powerful and clean ways of doing things in R.

PS : Be aware that you save the whole chisq.test object in your list. If you only need the value for Chi square or the p-value, select them first.

Upvotes: 4

Ari B. Friedman
Ari B. Friedman

Reputation: 72741

Fundamentally, you have a few problems here:

  1. You're relying heavily on global arguments rather than local ones. This makes the double usage of "data" confusing.

  2. Similarly, you rely on a hard-coded value (column 1) instead of passing it as an argument to the function.

  3. You're not extracting the one value you need from the chisq.test(). This means your result gets returned as a list.

  4. You didn't provide some example data. So here's some:

    m <- 10 n <- 4 mytable <- matrix(runif(m*n),nrow=m,ncol=n)

Once you fix the above problems, simply run a loop over various columns (since you've now avoided hard-coding the column) and store the result.

Upvotes: 4

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