setdiff datframes

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

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setdiff datframes

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