[R] strange output with merge function

[Ana Marija]

HI Jeff,

the issue got resolved after I converted data in as.data.frame.

Thank you for the useful input!

Ana

On Tue, Dec 3, 2019 at 12:46 PM Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:

> My guess would be that your key columns are factors with different levels.
> You have to be very careful manipulating factors... I recommend using
> character data until you are ready to do analysis steps that need factors.
> You may be able to resolve this by importing your data with the as.is=TRUE
> or stringsAsFactors=FALSE depending what functions you are using (read the
> help for your input function).
>
> On December 3, 2019 10:02:45 AM PST, Ana Marija <
> sokovic.anamarija using gmail.com> wrote:
> >Hi,
> >
> >I have two data frames like this:
> >
> >> head(a)
> >               V1    V2     V3     V4 V5   V6      V7          V8    V9
> > V10
> >1: ENSG00000272636 chr17 181637 181636  - 4924 -769472   rs7216126
> >chr17
> >951108
> >2: ENSG00000273172 chr17 191588 191587  - 4978   40553  rs62053745
> >chr17
> >151035
> >3: ENSG00000273172 chr17 191588 191587  - 4978   39501  rs77383171
> >chr17
> >152087
> >4: ENSG00000273172 chr17 191588 191587  - 4978   38817  rs34245596
> >chr17
> >152771
> >5: ENSG00000273172 chr17 191588 191587  - 4978   38580 rs112513622
> >chr17
> >153008
> >6: ENSG00000273172 chr17 191588 191587  - 4978   37794   rs8069278
> >chr17
> >153794
> >      V11         V12       V13 V14          V15  V16
> >1: 951108 4.03837e-05  0.429720   1 6.967229e-05 TRUE
> >2: 151035 1.42190e-08 -0.488594   0 7.139876e-05 TRUE
> >3: 152087 1.76913e-09 -0.664469   0 7.139876e-05 TRUE
> >4: 152771 2.04442e-08 -0.479176   0 7.139876e-05 TRUE
> >5: 153008 6.46268e-07 -0.768610   0 7.139876e-05 TRUE
> >6: 153794 1.95944e-08 -0.480011   0 7.139876e-05 TRUE
> >
> >
> >> head(f)
> >            V8
> >1:  rs12940868
> >2:   rs4383187
> >3:   rs4404112
> >4:   rs7214091
> >5:  rs35871790
> >6: rs112532541
> >
> >I am trying to merge with:
> >
> >m=merge(a,f,by="V8")
> >
> >but I am getting this output where column on which I am merging V8 is
> >replaced with number 17...
> >
> >> head(m)
> >V8              V1    V2     V3     V4 V5   V6    V7    V9    V10
> >V11
> >1: 17 ENSG00000273172 chr17 191588 191587  - 4978  1108 chr17 190480
> >190480
> >2: 17 ENSG00000273172 chr17 191588 191587  - 4978  1108 chr17 190480
> >190480
> >3: 17 ENSG00000273172 chr17 191588 191587  - 4978  1108 chr17 190480
> >190480
> >4: 17 ENSG00000262061 chr17 331206 331205  + 5858 24653 chr17 355858
> >355858
> >5: 17 ENSG00000262061 chr17 331206 331205  + 5858 24653 chr17 355858
> >355858
> >6: 17 ENSG00000262061 chr17 331206 331205  + 5858 24653 chr17 355858
> >355858
> >           V12       V13 V14          V15  V16
> >1: 8.23430e-09 -0.511644   0 7.139876e-05 TRUE
> >2: 8.23430e-09 -0.511644   0 7.139876e-05 TRUE
> >3: 8.23430e-09 -0.511644   0 7.139876e-05 TRUE
> >4: 5.46479e-05 -0.329785   0 5.962828e-05 TRUE
> >5: 5.46479e-05 -0.329785   0 5.962828e-05 TRUE
> >6: 5.46479e-05 -0.329785   0 5.962828e-05 TRUE
> >
> >Please advise,
> >Thanks
> >Ana
> >
> >       [[alternative HTML version deleted]]
> >
> >______________________________________________
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> >and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.
>

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