I have integratted data. Now i want to do supervised clustring based upon the list of specific genes(total 1112 genes as character vector). Following is code.
Gene_list
[1] "Mcc" "Ncan" "Thg1l" "Malat1" "Frmpd3" "Rbm47"
[7] "Ppcdc" "Olfr907" "Snrnp40" "Igf2bp3" "Bhlhe41" "EU599041"
[13] "Cst3" "Ccdc162" "Tug1" "Olfr66" "Mid1" "Dpysl2"
[19] "Csf1r" "Rps27rt" "Cask" "Hook3" "Sass6" "Eva1c"
[25] "Pi4kb" "Ppm1h" "Lin54" "C1qb" "Lasp1" "Rbm4b"
[31] "Adap2os" "B2m" "Olfr509" "Dock10" "Mrpl23-ps1" "Tnfrsf14"
[37] "Olfr1385" "C1qc" "P2ry12" "AW822252" "Olfr596" "Tpm3"
[43] "Slc10a2" "Ssbp2" "Ranbp3l" "Laptm5" "Ankrd11" "Olfr586"
[49] "Ccdc152" "Ctsd" "CT025600.1" "Slc25a53" "AI182371" "Tmem250-ps"
[55] "Dbhos" "Magi3" "Ddx23" "Olfr1305" "Psap" "Olfr1120"
[61] "Ift80" "Olfr986" "Fau-ps2" "CT025579.1" "Znrf3" "Xpnpep1"
[67] "Slc39a2" "Olfr825" "Irak1" "Tmem72" "Vmn1r180" "Olfr351"
[73] "Serinc3" "Vps39" "Olfr648" "mt-Nd5" "Pisd-ps2" "Cbx1"
[79] "Pecam1" "Eif2ak2" "Ltbp1" "Cx3cr1" "Olfr64" "Clasp2"
[85] "Pot1b" "Olfr734" "Olfr740" "Psg16" "Olfr1312" "Maip1"
[91] "Srd5a3" "Cep112it" "Skint8" "Gucy1a2" "CT009536.1" "Ostf1"
[97] "Neurl3" "Usp25" "Orc3" "Ccdc144b" "Prr15" "Slfn9"
[103] "Prdm11" "Vmn1r201" "CT009480.1" "Dynlt1c" "Uvrag" "Ces2f"
[109] "Olfr628" "Mef2a" "Nfia" "Zfp488" "Slc9a7" "Pm20d1"
[115] "Nox4" "Lyrm1" "Meg3" "CT010456.1" "Mrgpre" "CT009757.1"
[121] "Crp" "Trem2" "Olfr1245" "Colec12" "Ppnr" "CT030182.2"
[127] "Zfp979" "Rps6ka5" "Olfr1217" "Olfr1009" "Fdxacb1" "Lair1"
[133] "Olfr789" "Thsd7b" "CT025626.1" "Olfr767" "Prkcq" "Olfr667"
[139] "Cenpi" "Cd34" "Slfn3" "Six2" "Ctsb" "Sesn3"
[145] "Olfr432" "Zmat2" "CT025642.1" "Ipmk" "Cdkn1b" "Zfp369"
[151] "Vsir" "CT572985.1" "BC016548" "Itga4" "Olfr466" "Neil3"
[157] "Abcc1" "Slmapos2" "Naaa" "Fh1" "Prickle2" "Olfr1273-ps"
[163] "Klhl7" "E2f7" "Sec11a" "Rn7s1" "Rn7s2" "C1qa"
[169] "Olfr173" "Cd300lf" "Mpeg1" "Olfr1316" "Sox1ot" "Actn2"
[175] "Rab8b" "Zkscan2" "Mettl6" "Cul4a" "Mad2l1" "Cep97"
[181] "Rdh1" "Lipe" "Cd200r2" "Olfr735" "Ceacam3" "Kctd12"
[187] "Cntn1" "Olfr1402" "Olfr1278" "Ado" "Slc29a3" "Mylk"
[193] "Sfi1" "Noct" "Alkbh8" "Tgfbr1" "Vmn1r6" "Pvt1"
[199] "Tcf7l2" "Kdsr" "Hook2" "Olfr54" "Olfr1383" "Dnah17"
[205] "Alg9" "Lpl" "Rnf212" "Krit1" "Olfr49" "Olfr1220"
[211] "Olfr204" "CAAA01205117.1" "Pfkfb3" "Olfr1303" "Kcnj2" "Rfx7"
[217] "Ly6e" "Sytl4" "Frg1" "Olfr1286" "CT025610.1" "Mup9"
[223] "Acer3" "Nanos1" "Tcp11l2" "Vmn1r90" "Pde3b" "Slfn8"
[229] "Hmmr" "Eprn" "Olfr1330" "Olfr362" "Ttc41" "Olfr1537"
[235] "Olfr1129" "Olfr1505" "Ano4" "Olfr1352" "Atpaf2" "Senp7"
[241] "Olfr1297" "Tnfrsf11a" "Olfr600" "Elmod2" "Slc35c2" "Macrod2os1"
[247] "Olfr802" "Cux2" "Asb13" "Pikfyve" "Olfr624" "Lss"
[253] "Kdelr2" "Eif2a" "Rdh9" "Trim37" "Asb1" "Rplp1"
[259] "Sh2d1a" "Olfr1175-ps" "Siglech" "Ifit1bl2" "Bbof1" "Khdrbs2"
[265] "Jam2" "Olfr177" "Olfr365" "Ap1g1" "Casp4" "Nagk"
[271] "Vmn2r-ps54" "Sorbs1" "Olfr1160" "Tsga13" "D10Wsu102e" "Neu1"
[277] "Aspa" "Gucd1" "Panct2" "Brca2" "Tmem119" "Gbp5"
[283] "Eif4ebp1" "Fcgr3" "Arhgef5" "Serpine2" "Cnpy3" "Tyms"
[289] "Mill2" "Cenpc1" "Slco2b1" "Olfr243" "Olfr1216" "Vmn1r213"
[295] "Olfr829" "Pi15" "Olfr709-ps1" "Il6ra" "Olfr1269" "Vmn1r18"
[301] "Olfr510" "Trim24" "AI838599" "Slc6a1" "Tpgs2" "Cd84"
[307] "Olfr1233" "Zfp280d" "Olfr1459" "Cpa6" "Bora" "Triml1"
[313] "Gpr34" "Lcp2" "Rpia" "H2-K1" "Olfr75-ps1" "Lactb2"
[319] "Rag2" "Rpl13a" "Eea1" "Tbx5" "Slamf6" "Vmn1r173"
[325] "Tmem170" "Tbxas1" "Sgk3" "Scmh1" "Cxcl15" "Olfr472"
[331] "Olfr1310" "Cd40" "Chrnb3" "Ifi208" "Bmt2" "Rtp3"
[337] "Olfr716" "Zfp809" "Hdhd5" "Lcp1" "Olfr535" "Olfr715"
[343] "Ankrd44" "Adam12" "Socs6" "Syt17" "Gas8" "Speer4b"
[349] "Olfr354" "Cyb5r4" "Serpina9" "Esyt2" "Tmem126b" "Ube2e2"
[355] "Fmo5" "Mtr" "Olfr671" "Olfr1328" "Olfr1471" "Clec12a"
[361] "Map6" "Utp23" "Rassf2" "Vmn1r72" "Pde6a" "Phf14"
[367] "Cd59b" "Svep1" "Vmn1r9" "Olfr1262" "Olfr251" "Zfp981"
[373] "Uba1y" "Zfp992" "Cep128" "Fanci" "Alg5" "Acer2"
[379] "Maats1" "Olfr63" "Zbtb20" "Ermp1" "Cab39l" "Dcdc2c"
[385] "Ces2b" "Clec4a2" "Olfr1162" "Ctsz" "Speg" "Klf10"
[391] "Olfr1173" "Olfr575" "Acss3" "Tmeff2" "Dtnbos" "AI839979"
[397] "Cd33" "Comt" "Ptprc" "Olfr1020" "Il5ra" "Olfr645"
[403] "Ryr3" "Icosl" "Matn2" "Tbc1d32" "Tyrobp" "Vmn1r209"
[409] "Vmn1r169" "Arid1b" "Uggt2" "Lsm6" "Rnf165" "Xrcc4"
[415] "Hoxc9" "Nudt12" "Cdt1" "Adcy8" "Pkhd1" "Olfr554"
[421] "D5Ertd615e" "Slc12a8" "Kcnj15" "Maf" "Olfr851" "Lamb1"
[427] "CT009765.1" "Pnpla1" "Scfd2" "Olfr1226" "Pign" "Zfp101"
[433] "Sdccag8" "Olfr898" "Chmp4c" "Plod1" "CT033781.1" "Mrpl19"
[439] "Ralgps2" "Olfr1321" "Sirt2" "Chst1" "CAAA01139602.1" "Ly86"
[445] "Chpt1" "Olfr341" "Ldhd" "Vmn1r83" "Tigit" "Muc16"
[451] "Skap2" "Sparc" "Vmn1r203" "CT030185.1" "CT025566.1" "Plekhs1"
[457] "Dnah7b" "Cenpq" "Acsm2" "Tmem241" "Bin2" "Olfr804"
[463] "Spcs2" "Vmn1r185" "Apool" "Olfr1205" "CT009754.2" "Rnaseh2b"
[469] "Adi1" "Gnaq" "Ostn" "Plxdc2" "Dnah6" "Fcer2a"
[475] "Rsu1" "Slc13a1" "Ston2" "Mcoln1" "Vmn1r214" "Otog"
[481] "Cbx3" "Sp140" "CT025642.3" "Nipal4" "Olfr506" "Fndc5"
[487] "Olfr93" "Ciapin1" "Hes7" "AL607131.1" "Mycbp2" "Mbnl3"
[493] "Katnal2" "2610044O15Rik8" "Dock2" "Olfr109" "Scd4" "Ifi213"
[499] "Ptges" "Idi1" "Tmod2" "Olfr1192-ps1" "Olfr329-ps" "Olfr571"
[505] "BC035947" "Lockd" "Awat2" "Igsf11" "Cisd3" "Platr14"
[511] "Olfr721-ps1" "Mylk4" "Tnfrsf22" "Stx7" "Prss30" "Elmo1"
[517] "Abca8b" "Vmn1r58" "Olfr1416" "Rps9" "Tpk1" "Slc12a3"
[523] "Klhdc7a" "Pkd1" "Ccl28" "CT033774.1" "Olfr1309" "Zfp458"
[529] "Apol7b" "Ccdc82" "Ly6h" "Bglap3" "Caps2" "Vmn1r172"
[535] "Prkdc" "Vmn1r46" "Rps23" "Naalad2" "Cd81" "Mtfr1"
[541] "C6" "Pld4" "Pappa2" "Acbd6" "Rfx3" "Olfr1247"
[547] "Ntrk2" "Lingo2" "Platr10" "Pcdh15" "Abhd5" "Olfr676"
[553] "Tfpi" "Lrp2" "Csf2rb2" "Platr32" "CT009510.1" "CT030159.1"
[559] "Cngb1" "Olfr46" "Olfr681" "Cep162" "Ncstn" "Vmn1r77"
[565] "Lpcat2" "Ubtfl1" "Neurod6" "Platr15" "Etfdh" "CT025538.1"
[571] "Dock6" "Acaca" "Neil2" "Olfr1044" "Adgrv1" "Olfr536"
[577] "Prom1" "Dcx" "Olfr859" "Cracr2a" "Entpd7" "Dnajb11"
[583] "Pgpep1" "Abca9" "Pfas" "Trmt2b" "Igf1os" "Lmbrd1"
[589] "Canx" "Gpr174" "Lamb3" "Shprh" "Olfr1396" "Olfr1351"
[595] "Tpt1" "Gnaz" "BC026762" "Olfr1356" "Spta1" "Olfr1250"
[601] "Col26a1" "Cdc42" "Olfr905" "Zfp709" "Rbm45" "Olfr287"
[607] "Slc38a5" "Rap2b" "Snapc1" "Tmx4" "Piga" "Ugt3a1"
[613] "Hdac9" "Hspb11" "Pag1" "Necab1" "Pabpc4l" "Vmn1r198"
[619] "Ptgr2" "Asb18" "Rab3c" "CT025619.2" "Txk" "Isca1"
[625] "Ctsc" "Sult5a1" "Zfp300" "Arsk" "Tex9" "Dusp23"
[631] "Pde7b" "Zbtb49" "Nek11" "Rplp2" "Abca12" "Wdfy4"
[637] "Zfp943" "Svet1" "Olfr137" "Gga2" "Timp3" "Glrx2"
[643] "Zfp689" "Ddx6" "Fbxw28" "Ctla2a" "Mug1" "Lamp1"
[649] "Svil" "Olfr668" "Catsperb" "Nectin3" "Olfr2" "CT025624.1"
[655] "Olfr1209" "A2ml1" "Olfr1039" "Crot" "Polr3k" "Olfr237-ps1"
[661] "BC024139" "Vsx2" "Pam" "Nlrp10" "Cenpf" "Cep57"
[667] "Vmn1r70" "Msh4" "Apaf1" "Fan1" "Olfr157" "Pik3r5"
[673] "Tmbim6" "Fus" "Smpd3" "Ccr9" "Ccnk" "Nlrp9b"
[679] "Mroh2a" "Brip1" "Ttn" "Zfp950" "Insig1" "Vps50"
[685] "Mndal" "Dnajc1" "Prss55" "Paqr3" "Cwf19l2" "Olfr1372-ps1"
[691] "Olfr970" "Kyat1" "Olfr397" "Gtpbp4" "Cct7" "Dip2b"
[697] "Olfr77" "Kdm5d" "AW822073" "Vmn1r81" "Sqle" "Olfr56"
[703] "Olfr867" "Cetn4" "Olfr843" "Slit2" "Isoc2a" "B3gnt8"
[709] "Mgam" "Olfr1238" "Naip6" "Camk2a" "Olfr1161" "Intu"
[715] "Platr9" "Mettl3" "Vax2os" "Ano6" "Tcf7l1" "Pygl"
[721] "Olfr1156" "Sntb2" "Far2os1" "Dhx33" "Olfr695" "Slc7a1"
[727] "Kcnq3" "Klhl24" "Fubp1" "C87414" "Hivep3" "CT009601.1"
[733] "Cltc" "Zfp125" "Trim36" "Adcy10" "Olfr161" "Sord"
[739] "Iars" "Nyx" "Stx4a" "Lrrfip1" "Grm5" "Mecomos"
[745] "C4bp" "Il18rap" "Nin" "Olfr1260" "Mertk" "Dicer1"
[751] "Vps35" "Alg6" "Slc35a3" "Usp28" "Nckap5" "Olfr607"
[757] "Lyn" "Col14a1" "Cyfip1" "Olfr1346" "Dnah7c" "Fam124a"
[763] "Mtus1" "Cp" "Msto1" "Gss" "Gpr149" "Usp17la"
[769] "Rps15a" "Atm" "Fam32a" "Prrg1" "Senp1" "Cebpg"
[775] "Olfr1048" "Nav3" "Terf2ip" "St14" "Ufl1" "Slitrk2"
[781] "Olfr1028" "Med16" "Olfr845" "Cubn" "Rplp0" "Dnah7a"
[787] "Mcmdc2" "Pax1" "Agk" "Dnah14" "Vmn1r76" "Tanc2"
[793] "Zdhhc6" "Lacc1" "Nek7" "Trim30b" "Klhl20" "Olfr381"
[799] "Rex2" "Frem1" "Abca13" "BB123696" "Ankef1" "Pirt"
[805] "Atp10b" "Ccdc148" "Olfr1115" "Fam117b" "Mpdz" "Dlx6"
[811] "Med17" "C2cd3" "Stt3a" "Smo" "Zfp429" "Pole2"
[817] "Marf1" "Tcte2" "Olfr887" "Fyb" "Lrrc7" "Otx1"
[823] "Enpp3" "Zbed4" "Mettl13" "Spry2" "Ercc6l" "Zfp780b"
[829] "Gpatch2" "AI662270" "G3bp2" "Sik1" "Arhgap26" "Nup210"
[835] "Sis" "Kirrel3os" "Fermt1" "Ms4a7" "Vmn1r73" "Brpf1"
[841] "Dcst1" "Plekhm3" "Man2a1" "Cd8a" "Carmil1" "Trim27"
[847] "Prl7d1" "Acadsb" "Glmp" "Rgs3" "Trpm1" "Fcgr2b"
[853] "Ercc8" "Olfr1564" "Nipal3" "Olfr1381" "Olfr981" "Abcc2"
[859] "Ccdc30" "Cdc123" "Birc5" "Tmem260" "Frrs1" "Samd14"
[865] "Kl" "Heatr5a" "Olfr678" "Trim56" "Ogdhl" "Nup205"
[871] "Cyb5r3" "Pid1" "Gnb4" "Col25a1" "Myo1b" "Coro7"
[877] "Rdh12" "Zfp994" "Olfr801" "Hibch" "Cnga1" "Appbp2"
[883] "Ncf1" "Dok5" "Adcy4" "Ap4m1" "Ints6" "Daam1"
[889] "Isy1" "Pycr1" "Tspan3" "Synpo2" "Olfr720" "Cct6a"
[895] "Adgrd1" "Olfr1116" "Dhx40" "Dtna" "Ttll5" "Olfr487"
[901] "Olfr338" "Olfr1509" "Ispd" "Bnc2" "Gvin1" "Otoa"
[907] "Parp11" "Gsap" "Nt5e" "Depdc5" "Dnah5" "Pcnx"
[913] "Olfr808" "Hectd2" "Crb1-ps" "Zfp141" "Plrg1" "Rps11"
[919] "Rhox8" "Cyp2j5" "Phxr4" "Pzp" "Ermap" "Vmn1r197"
[925] "Fam169b" "Ccdc138" "Olfr273" "Zfp738" "Col4a1" "Kdelc2"
[931] "Olfr414" "Ppfia2" "Zfp932" "Tnfaip8" "Tmem254c" "Pard3"
[937] "Zufsp" "H2-DMb2" "Olfr525" "Zzz3" "Lrrc3" "Reg2"
[943] "Recql" "Ivns1abp" "Pnpla8" "Nsf" "Ctcfl" "Opcml"
[949] "Emc9" "Arpc2" "Kntc1" "Pdss2" "Trim52" "Rps5"
[955] "Tbc1d14" "Clcc1" "Chd9" "Pigx" "Actr2" "Cr2"
[961] "Klf3" "Rrm1" "Itga2" "Rnpep" "Zfp871" "Hacl1"
[967] "Cenph" "Myo1g" "Irgm1" "Olfr1178" "Olfr806" "Clec2e"
[973] "Otogl" "Pon2" "AI314278" "Ildr1" "Rhno1" "Vmn1r218"
[979] "Ddx58" "Vmn1r199" "Pmf1" "Plce1" "Casp6" "Psd4"
[985] "Olfr1423" "Nbas" "Kpna1" "Oca2" "Spag9" "Olfr1501"
[991] "Jak1" "Oas1b" "Vmn1r175" "Dhodh" "Ttk" "Thrb"
[997] "Ulk2" "Tacr1" "Zgrf1" "Olfr914"
[ reached getOption("max.print") -- omitted 112 entries ]
DefaultAssay(data_integrated) <- "integrated"
data_integrated <- RunPCA(data_integrated,
features = Gene_list,
approx=F, npcs = 30)
Warning: The following 1012 features requested have not been scaled (running reduction without them): Mcc, Ncan, Thg1l, Malat1, Frmpd3, Rbm47, Olfr907, Snrnp40, Igf2bp3, Bhlhe41, EU599041, Cst3, Ccdc162, Tug1, Olfr66, Mid1, Dpysl2, Csf1r, Rps27rt....
data_integrated <- RunUMAP(data_integrated, features = Gene_list, dims = NULL)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds
I am not sure should i scale data(as it is SCTtransformed data). and which default assay should be used.although i tried all different assays.
thanks in advance.
Huma
I want to do supervised clustering based upon the list of genes(around 1000).
But not successfull