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 [spurdl...@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 <drjimle...@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 <ycd...@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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