# [R] Changing sign of columns and values

anteneh asmare h@n@tezer@ @end|ng |rom gm@||@com
Mon Jun 13 09:22:19 CEST 2022

```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 using gmail.com> wrote:
> Hi Hana,
> This is a bit more difficult, but the same basic steps apply. See the
> 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:
>
>  "SNPID OA    EA
>  snp001        C     A
>  snp002        G     A
>  snp003        C     A
>  snp004        G     A
>  snp005        C     T",
>
>  "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",
>
> # 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 using 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 using 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 using gmail.com>
>> > Date: 6/12/22  6:43 AM  (GMT+03:00) To: hanatezera
>> > <hanatezera using gmail.com>
>> > Cc: r-help mailing list <r-help using 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 using 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 using gmail.com>>
>> > Date:
>> > 6/12/22 1:59 AM (GMT+03:00)> To: hanatezera <hanatezera using gmail.com>,
>> > r-help
>> > mailing list <r-help using r-project.org>> Subject: Re: [R] Changing sign of
>> > columns and values>> Hi Hana,> I think this is what you want:>> # first
>> > 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 using 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]]> >> > ______________________________________________> >
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