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

[Yuan Chun Ding]

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 allele 1 to allele 9 are considered as "short" allele, allele 10 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 the 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  

   tem <- as.data.frame(t(dat[i,,drop=F]))
  names(tem)<-"V1"
  tem <- tem[which(tem$V1!=""),,drop=F]
  tem2 <-separate(tem, col=V1, into=c("m1","m2"), convert = T)
  tem3 <-gather(tem2, marker, VNTR_repeats, m1:m2)
  tem4 <-as.data.frame(t(t(table(tem3$VNTR_repeats))))[,c(1,3)]
  tem4$Var1 <-as.numeric(as.character(tem4$Var1))
  tem4 <-tem4[order(tem4$Var1),]
  m<-
________________________________________
From: Abby Spurdle [spurdle.a using gmail.com]
Sent: Sunday, March 15, 2020 3:42 PM
To: Jim Lemon
Cc: Yuan Chun Ding; r-help mailing list
Subject: Re: [R] find multiple mode

I think people have misinterpreted the question.
The OP wants local maxima from the series.

The original series is frequencies, so your table is frequencies of frequencies.

A solution can be derived by looking at signs of the first and second
differences.
But there may be a simpler way????

On Mon, Mar 16, 2020 at 10:24 AM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> Hi Ding,
> Translating this into R code:
>
> freq<-c(1,2,5,5,10,4,4,8,1,1,8,8,2,4,3,1,2,1,1,138,149,14,1,1)
> > table(freq)
> freq
>  1   2   3   4   5   8  10  14 138 149
>  8   3   1   3   2   3   1   1   1   1
> > library(prettyR)
> > Mode(freq)
> [1] "1"
>
> You have a single modal value (1). If there were at most two ones, you
> would have three values (2,4,8) that could be considered multiple
> modes. What you seem to be doing is considering values that are not
> separated by commas as modes. Perhaps this is a formatting problem
> with your email.
>
> Jim
>
> On Mon, Mar 16, 2020 at 7:55 AM Yuan Chun Ding <ycding using coh.org> wrote:
> >
> > Hi R users,
> >
> > I want to find multiple modes (10, 8, 149) for the following vector.
> >
> > freq =1,2,5,5  10,4,4,8,1,1,8,8,2,4,3,1,2,1,1 138 149  14,1,1;
> >
> > any suggestion?
> >
> > Thank you,
> >
> > Ding
> >
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