On 6/1/20 5:40 PM, Ana Marija wrote:
Hi Jim,
thank you so much for getting back to me. I tried your code and this is
what I get:
dim(neu2)
[1] 3740988 9
dim(nep2)
[1] 3740988 9
dim(ret2)
[1] 3740001 9
I think I would need to have the same number of lines in all 3 data frames.
Can you please advise.
You should check for duplicated Marker values.
--
David
Cheers
Ana
On Mon, Jun 1, 2020 at 7:31 PM Jim Lemon <[email protected]> wrote:
Hi Ana,
Not too hard, but your example has all the "marker" fields in common.
So using a sample that will show the expected result:
neu1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N
1 100000012 1:100000012:G:T 0.229925 T G + 0.650403 1594
1 100000827 1:100000827:C:T 0.287014 T C + 0.955449 1594
1 100002713 1:100002713:C:T 0.097867 T C - 0.290455 1594
1 100002882 1:100002882:T:G 0.287014 G T + 0.955449 1594
1 100002991 1:100002991:G:A 0.097867 A G - 0.290455 1594
1 100004726 1:100004726:G:A 0.132058 A G + 0.115005 1594",
header=TRUE,stringsAsFactors=FALSE)
nep1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N
1 100000012 1:100000012:G:T 0.2300430 T G - 0.1420030 1641
1 100000827 1:100000827:C:T 0.2867150 T C - 0.2045580 1641
1 100002713 1:100002713:C:T 0.0975015 T C - 0.0555507 1641
1 100002882 1:100002882:T:G 0.2867150 G T - 0.2045580 1641
1 100002991 1:100002991:G:A 0.0975015 A G - 0.0555507 1641
1 100004726 1:100004727:G:A 0.1325410 A G - 0.8725660 1641",
header=TRUE,stringsAsFactors=FALSE)
ret1<-read.table(text="Chr BP Marker MAF A1 A2 Direction pValue N
1 100000012 1:100000012:G:T 0.2322760 T G - 0.230383 1608
1 100000827 1:100000827:C:T 0.2882460 T C - 0.120356 1608
1 100002713 1:100002713:C:T 0.0982587 T C - 0.272936 1608
1 100002882 1:100002882:T:G 0.2882460 G T - 0.120356 1608
1 100002991 1:100002992:G:A 0.0982587 A G - 0.272936 1608
1 100004726 1:100004727:G:A 0.1340170 A G - 0.594538 1608",
header=TRUE,stringsAsFactors=FALSE)
# merge the three data frames on "Marker"
nn1<-merge(neu1,nep1,by="Marker")
nn2<-merge(nn1,ret1,by="Marker")
# get the common "Marker" strings
Marker3<-nn2$Marker
# subset all three data frames on Marker3
neu2<-neu1[neu1$Marker %in% Marker3,]
nep2<-nep1[nep1$Marker %in% Marker3,]
ret2<-ret1[ret1$Marker %in% Marker3,]
Jim
On Tue, Jun 2, 2020 at 7:50 AM Ana Marija <[email protected]>
wrote:
Hello,
I have 3 data frames which have about 3.4 mill lines (but they don't have
exactly the same number of lines)...they look like this:
...
Is there is a way to create another 3 data frames, say neu2, nep2, ret2
which would only contain lines that have the same entries in Marker
column
for all 3 data frames?
Thanks
Ana
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
[email protected] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
