[R] setdiff datframes
nac
nac at sanger.ac.uk
Mon Jun 25 20:14:48 CEST 2012
thanks
it works brilliantly
wrote:
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> 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.
>>
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