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 <drjimlemon at 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 <hanatezera at 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 <hanatezera at 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 >> > <drjimlemon at gmail.com> >> > Date: 6/12/22 6:43 AM (GMT+03:00) To: hanatezera >> > <hanatezera at gmail.com> >> > Cc: r-help mailing list <r-help at 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$beta)mydfJimOn Sun, Jun 12, 2022 at 9:11 AM >> > hanatezera <hanatezera at gmail.com> wrote:>> Dear jim thanks for your >> > help! I >> > want to change also the value of OA and EF simultaneously.> For instance >> > i >> > am looking the data> mydf> IDnumber OA EA beta> 1 1 A C >> > 0.050> >> > 2 2 G A 0.098> 3 3 T G 0.789>> Best,> Hana>>>> >> > -------- >> > Original message --------> From: Jim Lemon <drjimlemon at gmail.com>> >> > Date: >> > 6/12/22 1:59 AM (GMT+03:00)> To: hanatezera <hanatezera at gmail.com>, >> > r-help >> > mailing list <r-help at r-project.org>> Subject: Re: [R] Changing sign of >> > columns and values>> Hi Hana,> I think this is what you want:>> # first >> > read >> > in your example> mydf<-read.table(text=> "IDnumber OA EA beta> 1 >> > C A -0.05> 2 G A 0.098> 3 G T >> > -0.789",> header=TRUE,stringsAsFactors=FALSE)> # check it> mydf> >> > IDnumber OA >> > EA beta> 1 1 C A -0.050> 2 2 G A 0.098> 3 3 >> > G >> > T -0.789> # change values of mydf$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 <hanatezera at 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 at 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. >
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 <hanatezera at 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 <drjimlemon at 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 <hanatezera at
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 <hanatezera at 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
>>> > <drjimlemon at gmail.com>
>>> > Date: 6/12/22 6:43 AM (GMT+03:00) To: hanatezera
>>> > <hanatezera at gmail.com>
>>> > Cc: r-help mailing list <r-help at 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$beta)mydfJimOn Sun, Jun 12, 2022
at 9:11 AM
>>> > hanatezera <hanatezera at gmail.com> wrote:>> Dear
jim thanks for your
>>> > help! I
>>> > want to change also the value of OA and EF simultaneously.>
For
>>> > instance
>>> > i
>>> > am looking the data> mydf> IDnumber OA EA beta> 1
1 A C
>>> > 0.050>
>>> > 2 2 G A 0.098> 3 3 T G 0.789>>
Best,> Hana>>>>
>>> > --------
>>> > Original message --------> From: Jim Lemon <drjimlemon
at gmail.com>>
>>> > Date:
>>> > 6/12/22 1:59 AM (GMT+03:00)> To: hanatezera <hanatezera
at gmail.com>,
>>> > r-help
>>> > mailing list <r-help at r-project.org>> Subject: Re:
[R] Changing sign of
>>> > columns and values>> Hi Hana,> I think this is what
you want:>> #
>>> > first
>>> > read
>>> > in your example> mydf<-read.table(text=>
"IDnumber OA EA beta> 1
>>> > C A -0.05> 2 G A 0.098> 3
G T
>>> > -0.789",> header=TRUE,stringsAsFactors=FALSE)> #
check it> mydf>
>>> > IDnumber OA
>>> > EA beta> 1 1 C A -0.050> 2 2 G A
0.098> 3
>>> > 3
>>> > G
>>> > T -0.789> # change values of mydf$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 <hanatezera at 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 at 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.
>>
>