Dear Jim, Good morning, hope you are doing very well, Here I want to
calculate the specific parameters based on the previous data. I have
attached below.
can you help me with r functions or code to solve the above equations
Kind regards,
Hana
On 6/13/22, Jim Lemon <drjimle...@gmail.com> wrote:
> Hi Hana,
> This is a bit more difficult, but the same basic steps apply. See the
> comments for an explanation.
> When you submit a problem like this, it is a lot easier if you send
> the output from "dput" (e.g. dput(df1)) or set your data frames up
> with "read.table" like I have done in the example below. It make it
> lots easier for anyone who wants to reply to see what your dataset
> looks like and input that dataset to devise a solution.
> I have made some assumptions about marking the rows to be altered and
> the arithmetic to do on those rows. What follows may not be as general
> a solution as you want:
>
> df1<-read.table(text=
> "SNPID OA EA
> snp001 C A
> snp002 G A
> snp003 C A
> snp004 G A
> snp005 C T",
> header=TRUE,stringsAsFactors=FALSE)
>
> df2<-read.table(text=
> "SNPID OA EA id00001 id00002 id00003 id00004 id00005
> snp001 A C 1.01 2 0.97 1.97 1.99
> snp002 A G 1.02 2 1 2 2
> snp003 C A 1 1.03 2 0 1
> snp004 A G 1.02 1.99 2 1.02 1.98
> snp005 C T 1 0 1.01 1 1",
> header=TRUE,stringsAsFactors=FALSE)
>
> # get a logical vector of the different XA values
> reversals<-df1$EA != df2$EA | df1$OA != df2$OA
> reversals
>
> # set a variable to the maximum value of idxxxxx
> # just to make the code easier to understand
> maxid<-2
>
> # create a copy of df2
> dfnew<-df2
>
> # now swap the XA columns and reflect the
> # idxxxxxx values of the rows in which
> # EA and OA are different between df1 and df2
> # here I have looped through the rows
> nrows<-dim(dfnew)[1]
> idcols<-4:8
> XAcols<-2:3
> for(i in 1:nrows) {
> if(reversals[i]) {
> dfnew[i,XAcols]<-rev(dfnew[i,XAcols])
> dfnew[i,idcols]<-maxid-dfnew[i,idcols]
> }
> }
>
> dfnew
>
> Jim
>
> On Mon, Jun 13, 2022 at 12:09 AM anteneh asmare <hanatez...@gmail.com>
> wrote:
>>
>> Dear Jim, Morning I have the same issue regarding comparing and
>> swapping the value of columns fro two different data frames.
>> I have the following two data frames
>> Data frame 1
>> "SNPID" "OA" "EA"
>> "snp001" "C" "A"
>> "snp002" "G" "A"
>> "snp003" "C" "A"
>> "snp004" "G" "A"
>> "snp005" "C" "T"
>>
>> Data frame 2
>> SNPID OA EA id00001 id00002 id00003 id00004 id00005
>> snp001 A C 1.01 2
>> 0.97
>> 1.97 1.99
>> snp002 A G 1.02 2
>> 1
>> 2 2
>> snp003 C A 1 1.03
>> 2
>> 0 1
>> snp004 A G 1.02 1.99
>> 2
>> 1.02 1.98
>> snp005 C T 1 0
>> 1.01
>> 1 1
>>
>> I want to if OA s and EAs in data frame 2 is the same as OAs and EAs
>> data frame 1 in such case I want to keep all information in data
>> fram2 as it is . However if OA s and EAs in data frame 2 is
>> different from OAs and EAs data frame 1, I want to change OA s and
>> EAs in data frame 2 to OAs and EAs data frame 1 and I want to
>> redefine the values of the dosages (ids) of the variant (the dosage d
>> for the i-th individual and the j-th variant would become d_ij
>> new=2-dij.
>> Dosage [j,]=2-dosage[j,]
>> My desire data frame looks like
>> Dataframe new
>> SNPID" "OA" "EA" id00001 id00002 id00003 id00004 id00005
>> "snp001" "C" "A" 2-1.01 2- 2 2- 0.97
>> 2-1.97
>> 2-1.99
>> "snp002" "G" "A" 2- 1.02 2- 2
>> 2-1
>> 2-2 2- 2
>> "snp003" "C" "A" 1 1.03
>> 2
>> 0 1
>> "snp004" "G" "A" 2-1.02 2-1.99
>> 2-2 2-1.02 2-1.98
>> "snp005" "C" "T" 1 0
>> 1.01 1 1
>> can you help me the r code for the above.
>> Kind regards,
>> Hana
>>
>>
>> On 6/12/22, hanatezera <hanatez...@gmail.com> wrote:
>> > Dear Jim, Thanks a lot this is exactly i am looking for.Stay safe and
>> > blessed !Best,Hana
>> > -------- Original message --------From: Jim Lemon
>> > <drjimle...@gmail.com>
>> > Date: 6/12/22 6:43 AM (GMT+03:00) To: hanatezera
>> > <hanatez...@gmail.com>
>> > Cc: r-help mailing list <r-help@r-project.org> Subject: Re: [R]
>> > Changing
>> > sign of columns and values Hi Hana,I didn't look closely. The simplest
>> > rule
>> > that I can see is that theletters (nucleotides?) should be swapped if
>> > there
>> > has been a signchange in the beta value.
>> > Therefore:mydf<-read.table(text="IDnumber OA EA beta1 C A
>> > -0.052 G A 0.0983 G T
>> > -0.789",header=TRUE,stringsAsFactors=FALSE)# logical vector marking the
>> > rows
>> > to be swappedswap_letters<-mydf$beta < 0# save the OA values to be
>> > swappednewEA<-mydf$OA[swap_letters]# change the OAs to
>> > EAsmydf$OA[swap_letters]<-mydf$EA[swap_letters]# set the relevant EA
>> > values
>> > to the old OA valuesmydf$EA[swap_letters]<-newEA# change the beta
>> > valuesmydf$beta<-abs(mydf$beta)mydfJimOn Sun, Jun 12, 2022 at 9:11 AM
>> > hanatezera <hanatez...@gmail.com> wrote:>> Dear jim thanks for your
>> > help! I
>> > want to change also the value of OA and EF simultaneously.> For instance
>> > i
>> > am looking the data> mydf> IDnumber OA EA beta> 1 1 A C
>> > 0.050>
>> > 2 2 G A 0.098> 3 3 T G 0.789>> Best,> Hana>>>>
>> > --------
>> > Original message --------> From: Jim Lemon <drjimle...@gmail.com>>
>> > Date:
>> > 6/12/22 1:59 AM (GMT+03:00)> To: hanatezera <hanatez...@gmail.com>,
>> > r-help
>> > mailing list <r-help@r-project.org>> Subject: Re: [R] Changing sign of
>> > columns and values>> Hi Hana,> I think this is what you want:>> # first
>> > read
>> > in your example> mydf<-read.table(text=> "IDnumber OA EA beta> 1
>> > C A -0.05> 2 G A 0.098> 3 G T
>> > -0.789",> header=TRUE,stringsAsFactors=FALSE)> # check it> mydf>
>> > IDnumber OA
>> > EA beta> 1 1 C A -0.050> 2 2 G A 0.098> 3 3
>> > G
>> > T -0.789> # change values of mydf$beta to absolute values>
>> > mydf$beta<-abs(mydf$beta)> mydf> IDnumber OA EA beta> 1 1 C A
>> > 0.050> 2 2 G A 0.098> 3 3 G T 0.789>> Jim>> On Sun,
>> > Jun
>> > 12, 2022 at 8:27 AM hanatezera <hanatez...@gmail.com> wrote:> >> > I
>> > have
>> > the following data set in data frameIDnumber OA EA
>> > beta1 C A -0.052
>> > G A 0.0983 G T
>> > -0.789....I want to change the sign of negative beta. If the negative
>> > value
>> > change to postive i want to switch its EA and OA.My desire result will
>> > beIDnumber OA EA beta1 A C
>> > 0.052 G A
>> > 0.0983 T G 0.789....Any one can
>> > help
>> > me with r codes? kind regards,Hana> > [[alternative HTML
>> > version
>> > deleted]]> >> > ______________________________________________> >
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see> >
>> > https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the
>> > posting
>> > guide http://www.R-project.org/posting-guide.html> > and provide
>> > commented,
>> > minimal, self-contained, reproducible code.
>
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