Dear, Jim I try the following codes but I got an error
Dfm1<-data.table(Dfm1)
# the names of the columns to be multiplied by BETA
ID_names <- paste0("ID",4:8)
# the names of the new columns that have been multiplied by beta
new_ID_names <- paste0("new_",ID_names)
##### Now with a simple command we get the desired multiplication
datfm[, (new_ID_names) := .SD *BETA, .SDcols = ID_names]
datfm
str(datfm)
##### The PRS for each individual can be calculated using the colSums
function in base R:
PRS<-Dfm1[, colSums(.SD), .SDcols = new_ID_names]
PRS
On 6/13/22, anteneh asmare <hanatez...@gmail.com> wrote:
> 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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