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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