[R] find multiple mode, sorry for not providing enough information

Yuan Chun Ding ycd|ng @end|ng |rom coh@org
Mon Mar 16 17:35:34 CET 2020

Hi Jim,

Yes, you are right.  I sorted the tem4$Var1 first, then find rising peaks in Freq variable from left to right.   I guess I probably need to define the minimal rising and drop on both side of a potential maxima, so avoid identifying really small rising peaks.  For example, I only want to identify the freq value of freq=10 (corresponding var1 = allele6), freq=8(var1=allele9),, freq=8( var1=allele12), and freq=149 (var1=allele23),  but ignore freq=4 (var10=allele15) and freq=2 (var1=allele18).

I am still working on it, any help would be really appreciated.

Thank you,


-----Original Message-----
From: Jim Lemon [mailto:drjimlemon using gmail.com] 
Sent: Monday, March 16, 2020 1:10 AM
To: Yuan Chun Ding; r-help mailing list
Subject: Re: [R] find multiple mode, sorry for not providing enough information

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Hi Ding,
While I was completely off the track in my first reply, the subsequent posts make your problem somewhat clearer. The way you state the problem suggests that the order of the values of "freq" is important.
That is, it is not just a matter of finding local maxima, but the direction in which you approach those maxima is important. For example. I might want to only identify maxima with at least four monotonically increasing values preceding them and a decrease of at least half the value of the maximum in the succeeding value. By breaking down the problem into a set of criteria, these can be implemented in a function that will search the values in one direction, returning the locations of maxima that fulfil those criteria.


On Mon, Mar 16, 2020 at 3:11 PM Yuan Chun Ding <ycding using coh.org> wrote:
> sorry, I just came back.
> Yes,  Abby's understanding is right.
> > tem4$Var1
>  [1]  1    3   4   5   6    7   8   9  10  11  12  13  14  15  16  17  18  20   21   22    23     24   25   31
> > tem4$Freq
>  [1]   1   2   5   5  10   4   4   8   1    1    8    8     2     4    3    1    2    1     1   138  149    14    1     1
> I have 2000 markers, this is just one example marker, the var1 is a VNTR marker with alleles 1, 3, 4 etc, a multi-allele marker; the corresponding frequency for each allele is 1,2 5 etc.  I want to convert this multi-allele marker to bi-allele markers by choosing a cutoff value; I would want the cut point to be allele 6 with frequency of 10, so  patients with allele 1 to allele 5 are considered as carrying "short" allele, allele 6 to 31 as "long" allele;  then sliding to next rsing frequency peak, allele 8 with frequency of 8, etc.
> maybe those rising peaks are not really multiple modes, but I want to do this type of data conversion.  I want to first determine m number of modes, then convert input dat file into m different input files, then perform Cox regression analysis for each converted file. I am stuck in the step of find out m rise peaks.
> Thank you,
> Ding


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