Dictionary style replace multiple items

r dataframe bioinformatics
Stedy picture Stedy · Sep 25, 2011 · Viewed 31.2k times · Source

I have a large data.frame of character data that I want to convert based on what is commonly called a dictionary in other languages.

Currently I am going about it like so:

foo <- data.frame(snp1 = c("AA", "AG", "AA", "AA"), snp2 = c("AA", "AT", "AG", "AA"), snp3 = c(NA, "GG", "GG", "GC"), stringsAsFactors=FALSE)
foo <- replace(foo, foo == "AA", "0101")
foo <- replace(foo, foo == "AC", "0102")
foo <- replace(foo, foo == "AG", "0103")

This works fine, but it is obviously not pretty and seems silly to repeat the replace statement each time I want to replace one item in the data.frame.

Is there a better way to do this since I have a dictionary of approximately 25 key/value pairs?

Answer

c.gutierrez picture c.gutierrez · Sep 11, 2014

If you're open to using packages, plyr is a very popular one and has this handy mapvalues() function that will do just what you're looking for:

foo <- mapvalues(foo, from=c("AA", "AC", "AG"), to=c("0101", "0102", "0103"))

Note that it works for data types of all kinds, not just strings.

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