Hello,
Using Jim's code, the following is vectorized and the result is
identical to the for loop result.
# create a copy of df2
dfnew2 <- df2
dfnew2[reversals, XAcols] <- rev(dfnew2[reversals, XAcols])
dfnew2[reversals, idcols] <- maxid - dfnew2[reversals, idcols]
identical(dfnew, dfnew2)
#[1] TRUE
Hope this helps,
Rui Barradas
Às 00:41 de 13/06/2022, Jim Lemon escreveu:
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.
______________________________________________
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.
______________________________________________
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.
