How to read data when some numbers contain commas as thousand separator?

Not sure about how to have read.csv interpret it properly, but you can use gsub to replace "," with "", and then convert the string to numeric using as.numeric:

y <- c("1,200","20,000","100","12,111")
as.numeric(gsub(",", "", y))
# [1]  1200 20000 100 12111

This was also answered previously on R-Help (and in Q2 here).

Alternatively, you can pre-process the file, for instance with sed in unix.