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 <jensras...@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
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