R help - Apr 2020 - matching doesn't work

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

On 2020-04-10 18:46 -0500, Ana Marija wrote:
> 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), ]
Yes, it seems like my tab separated values got converted to 
spaces ... so comma separated values seemed like a sane choice 
...

But ... I do not have all those specific files called here ... 
this seems very similar to what you had before ... what is it 
that does not work?  Do you get any errors here at all, or?

I am not sure what I am suppose to run from your codes.
Can you just send me lines of codes which I should run? (without part
where you are loading your data frames)
(assuming my files are as I showed them)

Or the whole idea was to remove sep=" " from everywhere?

On Fri, Apr 10, 2020 at 7:01 PM Rasmus Liland <jensrasmus at gmail.com>
wrote:
>
> On 2020-04-10 18:46 -0500, Ana Marija wrote:
> > 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), ]
>
> Yes, it seems like my tab separated values got converted to
> spaces ... so comma separated values seemed like a sane choice
> ...
>
> But ... I do not have all those specific files called here ...
> this seems very similar to what you had before ... what is it
> that does not work?  Do you get any errors here at all, or?