Actually, merge, intersect functions are for columns, as far as I know.

Suppose: You have 2 objects obj1 and obj2:

If you only want to separate the rows in common, you could use the following function:

rows_in_common <- function(x,y)
{
  a <- apply(x, 1, paste, collapse = "")
  b <- apply(y, 1, paste, collapse = "")
  c <- x[!a %in% b,]
  return(c)
}

You can obtain result then by:

result <- rows_in_common(x = obj1, y = obj2)

Another thing is, this question is not related to Bioinformatics. This is a programming related question. Please post programming related questions from next time to: http://stackoverflow.com/

If you are planning to analyze genomic ranges in R (great choice!) - GenomicRanges from Bioconductor is all what you need. And this introduction by Dave Tang is a very good start.

# At first you'll need to install it.
source("[http://bioconductor.org/biocLite.R](http://bioconductor.org/biocLite.R)")
biocLite("GenomicRanges")
library("GenomicRanges")

# Read in your data
data <- read.table("test.bed",header=F)
# Format it

# Read in and format second file

# And intersect
intersect(bed, bed2)

There is more documentation here.

This is called a join and the function is called merge in R

merge two files

I would suggest you start by a) learning to define your questions more precisely b) look at e.g. http://swirlstats.com/ or other online resources for R.