[R] Find peaks in histograms / Analysis of cumulative frequency

From: Ulrik Stervbo <ulriks_at_ruc.dk>
Date: Sat 15 Jul 2006 - 21:55:26 EST

Hello all,

I have some histograms of amount of DNA in some cells (DU145 cells overexpressing Bax and Bcl-xL for those who wish to know). The histograms show not only two peaks as expected, but three, indicating that some cells have more than normal amounts of DNA.

I am interested in knowing how much of the cell populations are in each peak as well as between.

I am not really sure how to go about it; I have been considering fitting a gaussian distribution to each peak and integrate the part between the peaks as described by Watson et al (1987 Cytometry 8:1-8). A more straight forward and more visual approach appears to be plotting the cumulative frequencies. In either case, I should like to find the peaks in the histogram automatically, as well as getting proper information about the peaks.

How would I go about finding peaks using R? Also I have really not been able to figure out how to fit a distribution.

Is there a way to analyse the cumulative frequencies? the knots() function appears to return far too many knots.

I am relatively new to R, but do have good programming experience, though I am mostly biologist.

Thank you in advance for any inputs.

PS. An example of the histogram can be found here<http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.png>

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