Dear List,

I have a question regarding the matchPWM function of Biostrings package. 

The help page for the function states that it requires a position weight matrix as an input. At the same time I found a post on the list giving a following example of the use of the function:

(quoting: 
		[BioC] matching transcription factor binding sites

		Herve Pages hpages at fhcrc.org 

		Sat Apr 19 02:41:03 CEST 2008)

		Suppose 'pwm' contains a Position Weight Matrix, let's say:

		pwm <- rbind(A=c( 1,  0, 19, 20, 18,  1, 20,  7),
                		C=c( 1,  0,  1,  0,  1, 18,  0,  2),
                		G=c(17,  0,  0,  0,  1,  0,  0,  3),
                		T=c( 1, 20,  0,  0,  0,  1,  0,  8))

		Note that this is just a standard integer matrix with the 4 DNA base letters
		as row names (having these row names is mandatory).
		m <- matchPWM(pwm, chr1, min.score="90%")

It seems to me that the matrix in this example is a position frequency matrix and not a position weight matrix (the difference between the two is explained nicely in: Applied Bioinformatics for the identification of regulatory elements; WW Wasserman&A Sandelin, Nat Rev Genet, 2004).

Could somebody clarify what is the expected input for this function?

Thanks in advance,

Zuzanna Makowska






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