String manipulations in R (May 10, 2005)

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As part of my efforts to analyze microarray data, I am finding that I need to do simple string manipulations in R. Here is a list of functions that might help.

• paste() combines several strings together into a single string.
• substr() selects substrings.
• format() makes a set of numbers print out more nicely.

There are several functions that will convert one string into another string.

• chartr() converts specific characters in a string to different characters.
• tolower() converts all the letters in a string to lower case.
• toupper() converts all the letters in a string to upper case.
• casefold() will perform either of the two conversions shown above.

Several functions help find matches between two lists.

• a %in% b returns a logical value of TRUE for each value of a which can be found somewhere in list b and FALSE if that value cannot be found.
• pmatch(), match(), charmatch() work similarly but with subtle variations.

Several functions will use regular expressions.

• grep() searches for matches to a pattern.
• strsplit() splits a string into several pieces.

A nice tutorial, by the way, on regular expressions is at:

• en.wikibooks.org/wiki/Programming:Perl_Regular_expressions

There are several string manipulation functions found in the limma package, including

• makeUnique() is found in the limma package and adds numbers to the ends of duplicate strings to give each one a unique name.
• trimWhiteSpace() is found in the limma package and removes leading and trailing blanks from a string.