Performs differential expression analysis using the limma package to identify significantly expressed genes across different cell types. Computes median expression levels of these significant genes to create a reference signature matrix.
Value
List containing: - `reference_matrix`: Data frame of median expression values for significantly expressed genes. - `G`: Number of probes used that resulted in the lowest condition number. - `condition_number`: Minimum condition number obtained. - `whole_matrix`: Matrix of median values across all samples.
Examples
dat <- matrix(rnorm(2000), nrow = 100)
rownames(dat) <- paste("Gene", 1:100, sep = "_")
colnames(dat) <- paste("Sample", 1:20, sep = "_")
pheno <- sample(c("Type1", "Type2", "Type3"), 20, replace = TRUE)
results <- generateRef_limma(dat, pheno)
print(results)
#> $reference_matrix
#> [1] Type1 Type2 Type3
#> <0 rows> (or 0-length row.names)
#>
#> $G
#> [1] 50
#>
#> $condition_number
#> [1] 0
#>
#> $whole_matrix
#> Type1 Type2 Type3
#> Gene_1 -3.502960e-01 -0.069601836 -0.370146624
#> Gene_2 2.685985e-01 0.059208651 0.075836973
#> Gene_3 -8.763115e-01 0.312058303 -0.152545773
#> Gene_4 -3.549884e-01 0.179047539 -0.020622229
#> Gene_5 -2.320709e-01 -0.262678090 0.330602226
#> Gene_6 1.151466e-01 -0.602030747 -1.069252172
#> Gene_7 6.541015e-02 0.117420548 -0.227624806
#> Gene_8 2.727289e-01 0.703001795 -0.275899218
#> Gene_9 5.683064e-01 -0.005087181 -0.729808806
#> Gene_10 4.594009e-01 -0.779880243 0.533685008
#> Gene_11 -5.502303e-01 0.385040501 -0.424865175
#> Gene_12 1.720136e-03 0.351996769 -0.158058937
#> Gene_13 -3.402926e-01 -0.168059235 -0.178463862
#> Gene_14 -5.161753e-01 0.045993767 -0.524372043
#> Gene_15 5.266697e-03 0.417240224 0.111038368
#> Gene_16 -5.908702e-01 0.020477665 -0.134347986
#> Gene_17 -3.329544e-01 0.595069071 -0.577898941
#> Gene_18 -5.192909e-01 0.123993539 0.371894882
#> Gene_19 -6.767065e-01 -0.106397594 0.623540463
#> Gene_20 4.611238e-01 -0.059918201 0.278374002
#> Gene_21 2.031379e-01 1.284800815 -0.134612834
#> Gene_22 5.215295e-01 -0.109079876 0.055944426
#> Gene_23 -1.598989e-01 -0.994479836 -0.004844437
#> Gene_24 -4.602964e-01 -0.199867235 0.406366471
#> Gene_25 2.587356e-01 0.753420372 0.928280305
#> Gene_26 5.928206e-01 0.435595444 0.125964082
#> Gene_27 -6.403511e-01 0.220506660 -0.106292769
#> Gene_28 2.167055e-01 0.150213368 -0.122163599
#> Gene_29 2.977136e-01 -0.012546975 0.157479548
#> Gene_30 -8.557442e-01 0.671853873 0.077342903
#> Gene_31 -5.353458e-01 0.601359844 0.093822156
#> Gene_32 6.124180e-01 0.054609574 -0.422872007
#> Gene_33 3.171691e-01 0.236595502 0.136823619
#> Gene_34 -4.838731e-01 -0.044471920 0.013903658
#> Gene_35 1.547656e-01 -0.534811163 -0.137579581
#> Gene_36 -9.190144e-01 -0.031219996 0.264011434
#> Gene_37 -2.486837e-01 -0.425911201 0.091283554
#> Gene_38 2.080257e-01 0.180822011 -0.404069682
#> Gene_39 -3.888222e-05 -0.560241851 -0.099720369
#> Gene_40 6.725611e-02 -0.571339759 0.219787376
#> Gene_41 7.290482e-01 0.373684804 0.482758609
#> Gene_42 3.451223e-01 0.735091630 0.168024801
#> Gene_43 2.231167e-01 0.057850704 -0.913005531
#> Gene_44 -3.140320e-02 -0.262894843 -0.175058128
#> Gene_45 -8.333821e-01 -0.294231849 -0.579026453
#> Gene_46 1.067362e-03 -0.339967488 -0.022015036
#> Gene_47 -3.766091e-01 0.618532252 -0.121476365
#> Gene_48 -2.066444e-01 0.402639185 -0.773844310
#> Gene_49 2.477232e-01 0.877530984 0.329200588
#> Gene_50 -3.987424e-01 -0.464882765 0.281819311
#> Gene_51 3.578568e-01 -0.836164804 -0.172836903
#> Gene_52 5.901957e-01 0.214424249 0.254068220
#> Gene_53 -1.104618e-01 0.305685156 0.890379626
#> Gene_54 -3.022576e-01 -1.183133966 -0.666705010
#> Gene_55 -1.831076e-01 -0.780501609 -0.677023065
#> Gene_56 1.277111e-01 0.219747430 0.010664862
#> Gene_57 1.160399e-01 0.629521384 -0.525321835
#> Gene_58 -3.635230e-01 -0.300852632 -0.213349406
#> Gene_59 -2.930877e-01 -0.636273494 0.253270150
#> Gene_60 -3.325496e-01 -0.645806382 -0.093001089
#> Gene_61 -1.139282e+00 -0.131307112 -0.229254725
#> Gene_62 3.263049e-01 0.042513309 0.103362815
#> Gene_63 5.574303e-01 -0.015876540 -0.161248545
#> Gene_64 -9.888091e-01 -0.631445134 -0.085891551
#> Gene_65 -2.460990e-01 -0.231484945 -0.421548024
#> Gene_66 7.858191e-01 -0.548731015 -0.491443047
#> Gene_67 -1.781785e-01 -0.468696015 0.545635528
#> Gene_68 3.561357e-01 -0.284903482 -0.288449296
#> Gene_69 -2.333460e-01 0.356334108 0.710110232
#> Gene_70 -3.170696e-01 -0.081589880 0.633333596
#> Gene_71 -2.284047e-01 -0.732566487 -0.010768077
#> Gene_72 -6.615776e-01 0.741194720 0.433158965
#> Gene_73 4.535271e-01 0.461566094 -0.060610081
#> Gene_74 5.094687e-01 -0.200147013 -0.678807619
#> Gene_75 -3.245077e-01 -0.173451330 -0.048064173
#> Gene_76 -1.474565e-01 0.793918367 -0.587684757
#> Gene_77 6.469226e-01 -0.277366228 -0.228406204
#> Gene_78 -4.494626e-01 0.430427805 -0.130421890
#> Gene_79 9.019831e-01 0.734458203 -0.037415014
#> Gene_80 4.017629e-01 -0.213887080 0.139471133
#> Gene_81 2.941686e-01 -0.246528493 -0.184526498
#> Gene_82 -3.323693e-01 0.195664504 -0.234463431
#> Gene_83 1.875159e-01 0.390576089 0.250899226
#> Gene_84 1.476251e-02 -0.234026744 0.466728667
#> Gene_85 1.737364e-01 -0.283973587 0.244262636
#> Gene_86 -2.032521e-01 -0.263158284 -0.253966134
#> Gene_87 -6.713319e-01 0.056004304 0.734512927
#> Gene_88 4.520024e-01 -0.182194333 -0.237734026
#> Gene_89 -1.203289e-01 -0.317360284 -0.136112157
#> Gene_90 3.891164e-01 -0.384798672 0.124378266
#> Gene_91 -1.036532e+00 0.330680560 0.175396079
#> Gene_92 4.601790e-02 -0.494699035 0.420861381
#> Gene_93 -8.855479e-01 0.099308427 0.683406456
#> Gene_94 5.244652e-01 -0.635206049 0.725598608
#> Gene_95 -7.683220e-01 -0.248303831 -0.577421345
#> Gene_96 3.249445e-01 0.367501231 -0.274480218
#> Gene_97 -1.294047e+00 0.482825594 0.374320874
#> Gene_98 -7.923611e-02 0.566919054 -0.210025808
#> Gene_99 2.979372e-01 0.541704658 -0.457483759
#> Gene_100 1.284161e+00 0.172659184 -0.539746145
#>