sorry, this is not a homework question although I am working at home now due to
COVID19 virus spreading in California. I tried to write a function to
convert input data file.
> 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
mode_format <-function (i) {
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: R-help [r-help-boun...@r-project.org] on behalf of Duncan Murdoch
[murdoch.dun...@gmail.com]
Sent: Sunday, March 15, 2020 4:20 PM
To: Abby Spurdle; Jim Lemon
Cc: r-help mailing list
Subject: Re: [R] find multiple mode
On 15/03/2020 6:42 p.m., Abby Spurdle wrote:
> 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????
Presumably this is a homework question. Your answer is perfect for one
of those; more detail would be inappropriate.
Duncan Murdoch
>
> 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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