[R] is there is a way to extract lines in between 3 files that are in common based on one column?

[Jim Lemon]

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 <sokovic.anamarija using gmail.com> 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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