[R] setdiff datframes
Rui Barradas
ruipbarradas at sapo.pt
Mon Jun 25 18:51:44 CEST 2012
Hello,
It is recomended to post data using dput(). Something like
dput(head(DF, 20)) # or 30
Then, paste the output of this command in a post.
Untested, but I think it should work:
# Create a logical index into 'example2'
ix <- example2$V1 %in% setdiff(example2$V1,example1$V1)
example2[ix, ] # which rows does it index?
You could also save the results of setdiff() and then see which of
example2$V1 are %in% it. If the data.frame has many rows, this way could
save some memory. (setdifff(9 gives only 2 character values, versus 2
TRUE plus n-2 FALSE).
Hope this helps,
Rui Barradas
Em 25-06-2012 17:37, nathalie escreveu:
> hi,
>
>
> I have 2 files example 1 and example 2 and would like to know what is in
> example2 and not in example1 (attached)
> V1 contain data which could be in duplicated which I am using as
> identifiers
>
> I used setdiff(example2$V1,example1$V1) to find the identifiers which
> are specific to example2:
> [1] "rs2276598" "rs17253672"
>
> I am looking for a way to get an output with all columns (V1 to V14)
> for these 2 identifiers....
>
> thanks for any suggestions
>
>
> format example1
> V1 V2 V3 V4 V5 V6
> 1 rs4685 2:198257795 C ENSG00000115524 ENST00000424674 Transcript
> 2 rs4685 2:198257795 C ENSG00000115524 ENST00000335508 Transcript
> 3 rs788018 2:198265526 G ENSG00000115524 ENST00000335508 Transcript
> 4 rs788023 2:198283305 C ENSG00000115524 ENST00000335508 Transcript
> 5 rs41284843 2:25536827 A ENSG00000119772 ENST00000406659 Transcript
> 6 rs41284843 2:25536827 A ENSG00000119772 ENST00000321117 Transcript
> 7 rs41284843 2:25536827 A ENSG00000119772 ENST00000264709 Transcript
> 8 rs41284843 2:25536827 A ENSG00000119772 ENST00000380756 Transcript
> 9 rs3729680 3:178927410 G ENSG00000121879 ENST00000263967 Transcript
> 10 rs61744960 4:106156163 A ENSG00000168769 ENST00000305737 Transcript
> 11 rs61744960 4:106156163 A ENSG00000168769 ENST00000413648 Transcript
> 12 rs61744960 4:106156163 A ENSG00000168769 ENST00000540549 Transcript
> 13 rs61744960 4:106156163 A ENSG00000168769 ENST00000545826 Transcript
> 14 rs61744960 4:106156163 A ENSG00000168769 ENST00000380013 Transcript
> 15 rs61744960 4:106156163 A ENSG00000168769 ENST00000535110 Transcript
> 16 rs61744960 4:106156163 A ENSG00000168769 ENST00000394764 Transcript
> 17 rs61744960 4:106156163 A ENSG00000168769 ENST00000513237 Transcript
> 18 rs61744960 4:106156163 A ENSG00000168769 ENST00000265149 Transcript
> 19 rs2454206 4:106196951 G ENSG00000168769 ENST00000540549 Transcript
> 20 rs2454206 4:106196951 G ENSG00000168769 ENST00000513237 Transcript
> V7 V8 V9 V10 V11 V12 V13
> 1 SYNONYMOUS_CODING 704 705 235 V gtA/gtG rs4685
> 2 SYNONYMOUS_CODING 3749 3657 1219 V gtA/gtG rs4685
> 3 SYNONYMOUS_CODING 2723 2631 877 G ggT/ggC rs788018
> 4 SYNONYMOUS_CODING 515 423 141 K aaA/aaG rs788023
> 5 SYNONYMOUS_CODING 365 27 9 P ccC/ccT
> rs41284843
> 6 SYNONYMOUS_CODING 264 27 9 P ccC/ccT
> rs41284843
> 7 SYNONYMOUS_CODING 365 27 9 P ccC/ccT
> rs41284843
> 8 NMD_TRANSCRIPT,SYNONYMOUS_CODING 264 27 9 P ccC/ccT
> rs41284843
> 9 NON_SYNONYMOUS_CODING 1330 1173 391 I/M atA/atG
> rs3729680
> 10 NON_SYNONYMOUS_CODING 1468 1064 355 G/D gGt/gAt
> rs61744960
> 11 NON_SYNONYMOUS_CODING 1204 1064 355 G/D gGt/gAt
> rs61744960
> 12 NON_SYNONYMOUS_CODING 1924 1064 355 G/D gGt/gAt
> rs61744960
> 13 NON_SYNONYMOUS_CODING 1924 1064 355 G/D gGt/gAt
> rs61744960
> 14 NON_SYNONYMOUS_CODING 1450 1064 355 G/D gGt/gAt
> rs61744960
> 15 NON_SYNONYMOUS_CODING 1167 1064 355 G/D gGt/gAt
> rs61744960
> 16 NON_SYNONYMOUS_CODING 1450 1064 355 G/D gGt/gAt
> rs61744960
> 17 NON_SYNONYMOUS_CODING 1924 1127 376 G/D gGt/gAt
> rs61744960
> 18 NMD_TRANSCRIPT,NON_SYNONYMOUS_CODING 1450 1064 355 G/D gGt/gAt
> rs61744960
> 19 NON_SYNONYMOUS_CODING 6144 5284 1762 I/V Ata/Gta
> rs2454206
> 20 NON_SYNONYMOUS_CODING 6144 5347 1783 I/V Ata/Gta
> rs2454206
> V14
> 1 ENSP=ENSP00000409435;HGNC=SF3B1
> 2 ENSP=ENSP00000335321;HGNC=SF3B1
> 3 ENSP=ENSP00000335321;HGNC=SF3B1
> 4 ENSP=ENSP00000335321;HGNC=SF3B1
> 5 ENSP=ENSP00000384852;HGNC=DNMT3A
> 6 ENSP=ENSP00000324375;HGNC=DNMT3A
> 7 ENSP=ENSP00000264709;HGNC=DNMT3A
> 8 ENSP=ENSP00000370132;HGNC=DNMT3A
> 9
> ENSP=ENSP00000263967;PolyPhen=benign(0.019);SIFT=tolerated(0.13);HGNC=PIK3CA
>
> 10
> ENSP=ENSP00000306705;PolyPhen=probably_damaging(0.983);SIFT=deleterious(0.01);HGNC=TET2
>
> 11
> ENSP=ENSP00000391448;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 12
> ENSP=ENSP00000442788;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 13
> ENSP=ENSP00000442867;PolyPhen=probably_damaging(0.952);SIFT=deleterious(0.01);HGNC=TET2
>
> 14
> ENSP=ENSP00000369351;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 15
> ENSP=ENSP00000438851;PolyPhen=probably_damaging(0.998);SIFT=deleterious(0.01);HGNC=TET2
>
> 16
> ENSP=ENSP00000378245;PolyPhen=probably_damaging(0.983);SIFT=deleterious(0.01);HGNC=TET2
>
> 17
> ENSP=ENSP00000425443;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 18
> ENSP=ENSP00000265149;PolyPhen=probably_damaging(0.952);SIFT=deleterious(0.01);HGNC=TET2
>
> 19
> ENSP=ENSP00000442788;PolyPhen=benign(0.029);SIFT=tolerated(0.15);HGNC=TET2
> 20
> ENSP=ENSP00000425443;PolyPhen=benign(0.029);SIFT=tolerated(0.15);HGNC=TET2
>
>
> > example2
> V1 V2 V3 V4 V5 V6
> 1 rs4685 2:198257795 C ENSG00000115524 ENST00000424674 Transcript
> 2 rs4685 2:198257795 C ENSG00000115524 ENST00000335508 Transcript
> 3 rs788018 2:198265526 G ENSG00000115524 ENST00000335508 Transcript
> 4 rs788023 2:198283305 C ENSG00000115524 ENST00000335508 Transcript
> 5 rs2276598 2:25469502 T ENSG00000119772 ENST00000321117 Transcript
> 6 rs2276598 2:25469502 T ENSG00000119772 ENST00000380756 Transcript
> 7 rs2276598 2:25469502 T ENSG00000119772 ENST00000402667 Transcript
> 8 rs2276598 2:25469502 T ENSG00000119772 ENST00000380746 Transcript
> 9 rs2276598 2:25469502 T ENSG00000119772 ENST00000264709 Transcript
> 10 rs3729680 3:178927410 G ENSG00000121879 ENST00000263967 Transcript
> 11 rs61744960 4:106156163 A ENSG00000168769 ENST00000305737 Transcript
> 12 rs61744960 4:106156163 A ENSG00000168769 ENST00000413648 Transcript
> 13 rs61744960 4:106156163 A ENSG00000168769 ENST00000540549 Transcript
> 14 rs61744960 4:106156163 A ENSG00000168769 ENST00000545826 Transcript
> 15 rs61744960 4:106156163 A ENSG00000168769 ENST00000380013 Transcript
> 16 rs61744960 4:106156163 A ENSG00000168769 ENST00000535110 Transcript
> 17 rs61744960 4:106156163 A ENSG00000168769 ENST00000394764 Transcript
> 18 rs61744960 4:106156163 A ENSG00000168769 ENST00000513237 Transcript
> 19 rs61744960 4:106156163 A ENSG00000168769 ENST00000265149 Transcript
> 20 rs17253672 4:106156187 T ENSG00000168769 ENST00000305737 Transcript
> V7 V8 V9 V10 V11 V12 V13
> 1 SYNONYMOUS_CODING 704 705 235 V gtA/gtG rs4685
> 2 SYNONYMOUS_CODING 3749 3657 1219 V gtA/gtG rs4685
> 3 SYNONYMOUS_CODING 2723 2631 877 G ggT/ggC rs788018
> 4 SYNONYMOUS_CODING 515 423 141 K aaA/aaG rs788023
> 5 SYNONYMOUS_CODING 1503 1266 422 L ctG/ctA
> rs2276598
> 6 NMD_TRANSCRIPT,SYNONYMOUS_CODING 1503 1266 422 L ctG/ctA
> rs2276598
> 7 SYNONYMOUS_CODING 745 597 199 L ctG/ctA
> rs2276598
> 8 SYNONYMOUS_CODING 813 699 233 L ctG/ctA
> rs2276598
> 9 SYNONYMOUS_CODING 1604 1266 422 L ctG/ctA
> rs2276598
> 10 NON_SYNONYMOUS_CODING 1330 1173 391 I/M atA/atG
> rs3729680
> 11 NON_SYNONYMOUS_CODING 1468 1064 355 G/D gGt/gAt
> rs61744960
> 12 NON_SYNONYMOUS_CODING 1204 1064 355 G/D gGt/gAt
> rs61744960
> 13 NON_SYNONYMOUS_CODING 1924 1064 355 G/D gGt/gAt
> rs61744960
> 14 NON_SYNONYMOUS_CODING 1924 1064 355 G/D gGt/gAt
> rs61744960
> 15 NON_SYNONYMOUS_CODING 1450 1064 355 G/D gGt/gAt
> rs61744960
> 16 NON_SYNONYMOUS_CODING 1167 1064 355 G/D gGt/gAt
> rs61744960
> 17 NON_SYNONYMOUS_CODING 1450 1064 355 G/D gGt/gAt
> rs61744960
> 18 NON_SYNONYMOUS_CODING 1924 1127 376 G/D gGt/gAt
> rs61744960
> 19 NMD_TRANSCRIPT,NON_SYNONYMOUS_CODING 1450 1064 355 G/D gGt/gAt
> rs61744960
> 20 NON_SYNONYMOUS_CODING 1492 1088 363 P/L cCt/cTt
> rs17253672
> V14
> 1 ENSP=ENSP00000409435;HGNC=SF3B1
> 2 ENSP=ENSP00000335321;HGNC=SF3B1
> 3 ENSP=ENSP00000335321;HGNC=SF3B1
> 4 ENSP=ENSP00000335321;HGNC=SF3B1
> 5 ENSP=ENSP00000324375;HGNC=DNMT3A
> 6 ENSP=ENSP00000370132;HGNC=DNMT3A
> 7 ENSP=ENSP00000384237;HGNC=DNMT3A
> 8 ENSP=ENSP00000370122;HGNC=DNMT3A
> 9 ENSP=ENSP00000264709;HGNC=DNMT3A
> 10
> ENSP=ENSP00000263967;PolyPhen=benign(0.019);SIFT=tolerated(0.13);HGNC=PIK3CA
>
> 11
> ENSP=ENSP00000306705;PolyPhen=probably_damaging(0.983);SIFT=deleterious(0.01);HGNC=TET2
>
> 12
> ENSP=ENSP00000391448;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 13
> ENSP=ENSP00000442788;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 14
> ENSP=ENSP00000442867;PolyPhen=probably_damaging(0.952);SIFT=deleterious(0.01);HGNC=TET2
>
> 15
> ENSP=ENSP00000369351;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 16
> ENSP=ENSP00000438851;PolyPhen=probably_damaging(0.998);SIFT=deleterious(0.01);HGNC=TET2
>
> 17
> ENSP=ENSP00000378245;PolyPhen=probably_damaging(0.983);SIFT=deleterious(0.01);HGNC=TET2
>
> 18
> ENSP=ENSP00000425443;PolyPhen=possibly_damaging(0.825);SIFT=deleterious(0);HGNC=TET2
>
> 19
> ENSP=ENSP00000265149;PolyPhen=probably_damaging(0.952);SIFT=deleterious(0.01);HGNC=TET2
>
> 20
> ENSP=ENSP00000306705;PolyPhen=possibly_damaging(0.602);SIFT=deleterious(0);HGNC=TET2
>
>
>
>
>
>
>
>
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