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
On 2020-04-10 17:05 -0500, Ana Marija wrote:> it didn't work unfortunately with your > example: > > > plink.genome[idx,] > character(0)Hi! Perhaps csv formatting are better suited for these emails ... the two ibdlist lines I added still matches in this example, added lookup for kinship ... see if this works for you: plink.genome <- "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" plink.genome <- read.csv(text=plink.genome) 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.csv(text=ibdlist) x <- paste(plink.genome$IID1, plink.genome$IID2) table <- paste(ibdlist$ID1, ibdlist$ID2) idx <- match(x=x, table=table) ibdlist[idx,"kinship"] Best, Rasmus
so if I understand correctly you would just remove sep=" " from my
codes?
Thank you so much for working on this.
Is there is any chance you can change my original code (pasted bellow)
with changes you think should work?
library(SNPRelate)
# get PLINK output
plink.genome <- read.table("plink.genome", header=TRUE)
snpgdsBED2GDS("output4.bed",
"output4.fam","output4.bim", "HapMap.gds")
genofile <- snpgdsOpen("HapMap.gds")
# get SNPRelate output
ibd <- snpgdsIBDMoM(genofile, remove.monosnp=FALSE, kinship=TRUE)
# adjust for the orders of sample pair
pair.samp <- paste(ibdlist$ID1, ibdlist$ID2, sep=" ")
plink.genome <- plink.genome[match(
paste(plink.genome$IID1, plink.genome$IID2, sep=" "), pair.samp),
]
On Fri, Apr 10, 2020 at 6:03 PM Rasmus Liland <jensrasmus at gmail.com>
wrote:>
> On 2020-04-10 17:05 -0500, Ana Marija wrote:
> > it didn't work unfortunately with your
> > example:
> >
> > > plink.genome[idx,]
> > character(0)
>
> Hi! Perhaps csv formatting are better
> suited for these emails ... the two
> ibdlist lines I added still matches in
> this example, added lookup for kinship
> ... see if this works for you:
>
>
> plink.genome <-
"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"
> plink.genome <- read.csv(text=plink.genome)
>
> 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.csv(text=ibdlist)
>
> x <- paste(plink.genome$IID1, plink.genome$IID2)
> table <- paste(ibdlist$ID1, ibdlist$ID2)
> idx <- match(x=x, table=table)
> ibdlist[idx,"kinship"]
>
>
> Best,
> Rasmus