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@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. >> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ______________________________________________ R-help@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.
