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

Jeff Newmiller jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Mon Mar 16 06:42:16 CET 2020 

Anyone following along on the mailing list cannot see your "red text" since this is a plain text mailing list.

Please set your email format to "plain text" when sending messages to the R mailing lists so you don't fool yourself into thinking we can see HTML formatting. It will also avoid corrupting your code examples... which does happen sometimes with formatted emails.

On March 15, 2020 10:00:25 PM PDT, Yuan Chun Ding <ycding using coh.org> wrote:
>
>
>You **might** do better pursuing this sort of thing on the Bioconductor
>site:
>https://www.bioconductor.org/help/<https://urldefense.com/v3/__https://www.bioconductor.org/help/__;!!Fou38LsQmgU!441uqddHFvpuq6wfAy-jNNUZ8Dz_jGxN9itKerhoPxav-yjaqUkpwPhN4bJJ$>
>They often have professionally written R packages tailored for genomics
>so that you don't need to shake and bake your own with all the dangers
>that entails (not least of which may be that your methodology is
>suspect).
>
>Bert Gunter
>
>"The trouble with having an open mind is that people keep coming along
>and sticking things into it."
>-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>Thank you, Bert!
>
>I just realized that I made a typo in the following email, so I
>modified it using the red font.  we are doing genomics work, but this
>is a understudied genomic research, so no professional packages. I
>admit that what I am doing is pretty explorative.
>
>On Sun, Mar 15, 2020 at 9:11 PM Yuan Chun Ding
><ycding using coh.org<mailto:ycding using coh.org>> wrote:
>sorry, I just came back.
>
>Yes,  Abby's understanding is right.
>
>> tem4$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$Freq
>[1]   1   2   5   5  10   4   4   8   1    1    8    8    2    4    3  
> 1    2    1     1   138  149    14    1     1
>
>I have 2000 markers, this is just one example marker, the var1 is a
>VNTR marker with alleles 1, 3, 4 etc, a multi-allele marker; the
>corresponding frequency for each allele is 1,2 5 etc.  I want to
>convert this multi-allele marker to bi-allele markers by choosing a
>cutoff value; I would want the cut point to be allele 6 with frequency
>of 10, so allele 1 to allele 5 are considered as "short" allele, allele
>6 to 31 as "long" allele;  then sliding to next rsing frequency peak,
>allele 8 with frequency of 8, etc.
>
>maybe those rising peaks are not really multiple modes, but I want to
>do this type of data conversion.  I want to first determine the number
>of modes, then convert input dat file into m different input files,
>then perform Cox regression analysis for each converted file. I am
>stuck in the step of find out m rise peaks.
>
>Thank you,
>
>Ding
>
>   tem <- as.data.frame(t(dat[i,,drop=F]))
>  names(tem)<-"V1"
>  tem <- tem[which(tem$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<mailto: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<mailto: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<mailto: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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