[R] matching doesn't work

Ana Marija
Fri, 10 Apr 2020 22:05:19 -0000

it didn't work unfortunately with your example:

> plink.genome[idx,]
character(0)

here is my whole:
plink.genome <- read.table("plink.genome", header=TRUE)

    FID1   IID1     FID2   IID2 RT    EZ      Z0      Z1      Z2
PI_HAT PHE       DST     PPC   RATIO    IBS0    IBS1    IBS2  HOMHOM
HETHET
  fam1054  G1054  fam1054   G700 OT     0  0.0045  0.9938  0.0017
0.4986  -1  0.839150  1.0000 209.7368     103  118630  250667 19.0000
3985.0000
  fam1054  G1054  fam1054   G701 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.838381  1.0000 266.0667      81  119124  249829 15.0000
3991.0000
  fam1079  G1079  fam2484  G2484 UN    NA  0.0000  0.0007  0.9993
0.9997  -1  0.999889  1.0000      NA       0      82  370250  0.0000
4591.0000
  fam1245  G1237  fam1245  G1245 OT     0  0.0036  0.9964  0.0000
0.4982  -1  0.838770  1.0000 188.4762      83  118647  249728 21.0000
3958.0000
  fam1245  G1241  fam1245  G1245 OT     0  0.0042  0.9854  0.0104
0.5031  -1  0.840569  1.0000 265.8667      97  117116  250690 15.0000
3988.0000
  fam0176   G174  fam0176   G176 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.837799  1.0000 190.0476     107  118306  246937 21.0000
3991.0000
  fam0176   G175  fam0176   G176 OT     0  0.0045  0.9909  0.0046
0.5001  -1  0.839611  1.0000 198.6500     102  117026  248327 20.0000
3973.0000
  fam0179   G177  fam0179   G179 OT     0  0.0091  0.9903  0.0006
0.4958  -1  0.838517  1.0000 116.5000     207  117568  247532 34.0000
3961.0000
  fam0179   G178  fam0179   G179 OT     0  0.0098  0.9902  0.0000
0.4951  -1  0.838160  1.0000 90.4318     224  117440  246548 44.0000
3979.0000
  fam1818  G1818  fam1818  G1819 OT     0  0.0050  0.9884  0.0066
0.5008  -1  0.839882  1.0000 208.8947     115  117679  250401 19.0000
3969.0000
  fam1818  G1818  fam1818  G1820 OT     0  0.0050  0.9950  0.0000
0.4975  -1  0.838709  1.0000 208.6842     115  119083  250671 19.0000
3965.0000
  fam2450  G2007  fam2450  G2450 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.831786  1.0000 79.0196     278  120248  238553 51.0000
4030.0000
  fam2450  G2024  fam2450  G2450 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.832052  1.0000 104.6750     242  118317  235124 40.0000
4187.0000
  fam2181  G2181  fam5745  G5745 UN    NA  0.0002  0.0034  0.9964
0.9981  -1  0.999402  1.0000      NA       4     432  367475  0.0000
4613.0000
  fam2183  G2183  fam2183  G2184 OT     0  0.0058  0.9836  0.0106
0.5024  -1  0.840452  1.0000 164.9583     133  117858  252192 24.0000
3959.0000
  fam2183  G2183  fam2183  G2185 OT     0  0.0045  0.9929  0.0026
0.4990  -1  0.839280  1.0000 136.2414     105  118760  251251 29.0000
3951.0000
  fam2280  G2280  fam2280  G2281 OT     0  0.0042  0.9893  0.0065
0.5011  -1  0.839937  1.0000 248.7500      97  117600  250265 16.0000
3980.0000
  fam2280  G2280  fam2280  G2282 OT     0  0.0033  0.9885  0.0082
0.5024  -1  0.840294  1.0000 264.8000      76  117095  249900 15.0000
3972.0000
  fam2286  G2284  fam2286  G2286 OT     0  0.0048  0.9952  0.0000
0.4976  -1  0.838745  1.0000 179.5909     112  118986  250534 22.0000
3951.0000
  fam2286  G2285  fam2286  G2286 OT     0  0.0046  0.9846  0.0108
0.5031  -1  0.840586  1.0000 331.4167     105  116441  249328 12.0000
3977.0000
  fam2813  G2813  fam4274  G4274 UN    NA  0.0058  0.0495  0.9447
0.9695  -1  0.990555  1.0000 239.2105     131    6616  357351 19.0000
4545.0000
  fam3238  G3237  fam3238  G3238 OT     0  0.0055  0.9913  0.0033
0.4989  -1  0.839299  1.0000 160.6800     125  117652  249060 25.0000
4017.0000
  fam3238  G3238  fam3238  G3264 OT     0  0.0035  0.9855  0.0110
0.5037  -1  0.840733  1.0000 173.3043      81  116986  250706 23.0000
3986.0000
  fam4257  G4257  fam0891   G891 UN    NA  0.2323  0.4978  0.2699
0.5188  -1  0.859862  1.0000 10.1332    5314   92050  268982 383.0000
3881.0000
  fam4275  G4275  fam4275  G4304 OT     0  0.0053  0.9947  0.0000
0.4973  -1  0.837959  1.0000 136.0345     122  118563  247910 29.0000
3945.0000
  fam4275  G4275  fam4275  G4352 OT     0  0.0048  0.9798  0.0154
0.5053  -1  0.841317  1.0000 209.3684     110  116482  251129 19.0000
3978.0000
  fam4454  G4452  fam4454  G4454 OT     0  0.0055  0.9840  0.0104
0.5024  -1  0.840440  1.0000 136.8966     127  116709  249681 29.0000
3970.0000
  fam4454  G4453  fam4454  G4454 OT     0  0.0057  0.9842  0.0101
0.5022  -1  0.840379  1.0000 160.0000     130  116255  248588 25.0000
4000.0000
  fam4666  G4666  fam0686   G686 UN    NA  0.0000  0.0026  0.9974
0.9987  -1  0.999576  1.0000      NA       0     312  367735  0.0000
4580.0000
  fam4691  G4691  fam4722  G4722 UN    NA  0.3986  0.4841  0.1173
0.3593  -1  0.818992  1.0000  5.9269    9073  113787  241580 602.0000
3568.0000
  fam5092  G5089  fam5092  G5092 OT     0  0.0051  0.9928  0.0022
0.4985  -1  0.839156  1.0000 234.4706     117  118225  249900 17.0000
3986.0000
  fam5092  G5092  fam5092  G5097 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.837560  1.0000 218.9444     100  119554  248956 18.0000
3941.0000
  fam5365  G5106  fam5365  G5365 OT     0  0.0057  0.9916  0.0027
0.4985  -1  0.839191  1.0000 208.0000     131  118747  251154 19.0000
3952.0000
  fam5365  G5118  fam5365  G5365 OT     0  0.0052  0.9886  0.0061
0.5004  -1  0.839781  1.0000 164.8750     121  118035  250954 24.0000
3957.0000
  fam0523   G523  fam0523   G551 OT     0  0.0037  0.9829  0.0135
0.5049  -1  0.841107  1.0000 180.6818      85  116769  251126 22.0000
3975.0000
  fam0523   G523  fam0523   G552 OT     0  0.0000  1.0000  0.0000
0.5000  -1  0.838173  1.0000 225.2353      81  119148  249406 17.0000
3829.0000
  fam5282  G5282  fam5282  G5328 OT     0  0.0033  0.9933  0.0035
0.5001  -1  0.839545  1.0000 232.1765      75  117898  249882 17.0000
3947.0000
  fam5681  G5681  fam0587   G587 UN    NA  0.0035  0.9871  0.0094
0.5030  -1  0.840482  1.0000 188.9524      79  116708  249522 21.0000
3968.0000
  fam0578   G578  fam6039  G6039 UN    NA  0.0000  0.0095  0.9905
0.9952  -1  0.998462  1.0000 4553.0000       1    1123  364629  1.0000
4553.0000

On Fri, Apr 10, 2020 at 4:24 PM Rasmus Liland <jensrasmus at gmail.com>
wrote:
>
> On 2020-04-10 15:38 -0500, Ana Marija wrote:
> | Hi,
> |
> | I have this code:
>
> Dear Ana,
>
> none of the ID tuples in the head
> outputs you provided matches, so I added
> two lines in ibdlist that matches up;
> perhaps if you provided more lines that
> would have matched in a pastebin
> somewhere ...
>
>
> options(stringsAsFactors=FALSE)
> plink.genome <-
> "FID1   IID1    FID2    IID2    RT      EZ      Z0      Z1      Z2
PI_HAT  PHE     DST
> fam1054 G1054   fam1054 G700    OT      0       0.0045  0.9938  0.0017
0.4986  -1      0.839150
> fam1054 G1054   fam1054 G701    OT      0       0.0000  1.0000  0.0000
0.5000  -1      0.838381
> fam1079 G1079   fam2484 G2484   UN              0.0000  0.0007  0.9993
0.9997  -1      0.999889
> fam1245 G1237   fam1245 G1245   OT      0       0.0036  0.9964  0.0000
0.4982  -1      0.838770
> fam1245 G1241   fam1245 G1245   OT      0       0.0042  0.9854  0.0104
0.5031  -1      0.840569
> fam0176 G174    fam0176 G176    OT      0       0.0000  1.0000  0.0000
0.5000  -1      0.837799"
>
> plink.genome <-
> read.delim(text=plink.genome, header=TRUE)
>
> ibdlist <-
> "ID1    ID2     k0      k1      kinship
> G1000   G1001   1.0000000       0.00000000      0.000000000
> G1000   G1003   0.9938901       0.00000000      0.003054932
> G1241   G1245   1.0000000       0.00000000      0.000000000
> G1000   G1005   1.0000000       0.00000000      0.000000000
> G1079   G2484   0.9938901       0.00000000      0.003054932
> G1000   G1009   1.0000000       0.00000000      0.000000000"
> ibdlist <-
> read.delim(text=ibdlist)
>
> idx <-
> match(paste(plink.genome$IID1, plink.genome$IID2),
>   paste(ibdlist$ID1, ibdlist$ID2))
> plink.genome[idx,]
>
>
> See if this fits the rest of your
> data.frames ...  Did I nail it here, or?
>
> Best,
> Rasmus