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 <jensras...@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
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