Compute pairwise alteration statistics for an alteration landscape
Source:R/selectX_stats.r
al.pairwise.alteration.stats.RdCompute pairwise alteration statistics for an alteration landscape
Examples
# \donttest{
data(luad_run_data, package = "SelectSim")
result <- selectX(M = luad_run_data$M,
sample.class = luad_run_data$sample.class,
alteration.class = luad_run_data$alteration.class,
n.cores = 1, min.freq = 10, n.permut = 10,
verbose = FALSE)
al.pairwise.alteration.stats(result$obj)
#> $overlap
#> 23 x 23 Matrix of class "dsyMatrix"
#> ARID1A ATM BRAF CDKN2A CMTR2 CTNNB1 EGFR KEAP1 KRAS MGA NF1 PIK3CA
#> ARID1A 18 1 0 2 1 2 3 2 5 2 1 0
#> ATM 1 22 1 1 1 0 1 0 13 0 2 0
#> BRAF 0 1 35 1 1 3 2 1 2 4 2 3
#> CDKN2A 2 1 1 17 1 0 3 1 3 0 1 1
#> CMTR2 1 1 1 1 17 0 2 0 6 2 0 0
#> CTNNB1 2 0 3 0 0 13 2 1 1 0 0 0
#> EGFR 3 1 2 3 2 2 57 0 0 3 1 2
#> KEAP1 2 0 1 1 0 1 0 33 13 1 4 1
#> KRAS 5 13 2 3 6 1 0 13 154 5 4 4
#> MGA 2 0 4 0 2 0 3 1 5 25 0 1
#> NF1 1 2 2 1 0 0 1 4 4 0 32 1
#> PIK3CA 0 0 3 1 0 0 2 1 4 1 1 20
#> PTPRD 1 1 2 3 2 0 2 1 2 1 0 0
#> PTPRT 2 1 1 1 1 0 1 1 2 0 0 0
#> RB1 1 0 2 0 1 0 2 1 2 2 2 2
#> RBM10 0 1 3 2 2 2 4 1 16 2 2 0
#> SETBP1 0 0 1 0 0 0 0 1 4 2 1 0
#> SETD2 2 0 5 0 0 1 3 2 4 0 1 2
#> SMAD4 3 0 2 2 1 0 4 0 1 1 1 0
#> SMARCA4 1 1 1 2 0 1 0 3 2 0 1 1
#> STK11 1 7 2 3 0 1 0 10 28 3 3 1
#> TP53 8 4 19 12 9 2 32 10 49 12 22 11
#> U2AF1 0 0 1 0 0 0 0 0 6 0 1 0
#> PTPRD PTPRT RB1 RBM10 SETBP1 SETD2 SMAD4 SMARCA4 STK11 TP53 U2AF1
#> ARID1A 1 2 1 0 0 2 3 1 1 8 0
#> ATM 1 1 0 1 0 0 0 1 7 4 0
#> BRAF 2 1 2 3 1 5 2 1 2 19 1
#> CDKN2A 3 1 0 2 0 0 2 2 3 12 0
#> CMTR2 2 1 1 2 0 0 1 0 0 9 0
#> CTNNB1 0 0 0 2 0 1 0 1 1 2 0
#> EGFR 2 1 2 4 0 3 4 0 0 32 0
#> KEAP1 1 1 1 1 1 2 0 3 10 10 0
#> KRAS 2 2 2 16 4 4 1 2 28 49 6
#> MGA 1 0 2 2 2 0 1 0 3 12 0
#> NF1 0 0 2 2 1 1 1 1 3 22 1
#> PIK3CA 0 0 2 0 0 2 0 1 1 11 0
#> PTPRD 14 3 0 1 0 0 2 1 2 4 1
#> PTPRT 3 13 0 1 0 1 1 2 2 6 0
#> RB1 0 0 19 0 0 1 0 1 1 15 0
#> RBM10 1 1 0 29 1 1 0 0 4 7 0
#> SETBP1 0 0 0 1 11 0 0 1 1 8 1
#> SETD2 0 1 1 1 0 22 2 2 2 5 1
#> SMAD4 2 1 0 0 0 2 14 0 0 6 0
#> SMARCA4 1 2 1 0 1 2 0 24 3 13 0
#> STK11 2 2 1 4 1 2 0 3 59 13 0
#> TP53 4 6 15 7 8 5 6 13 13 221 5
#> U2AF1 1 0 0 0 1 1 0 0 0 5 12
#>
#> $w_overlap
#> 23 x 23 Matrix of class "dsyMatrix"
#> ARID1A ATM BRAF CDKN2A CMTR2 CTNNB1
#> ARID1A 13.9848184 0.3225806 0.0000000 0.7225806 0.7692308 1.4545455
#> ATM 0.3225806 17.7580202 0.6250000 0.3225806 0.3571429 0.0000000
#> BRAF 0.0000000 0.6250000 26.8501591 0.6250000 0.4000000 2.7692308
#> CDKN2A 0.7225806 0.3225806 0.6250000 12.2348184 0.6250000 0.0000000
#> CMTR2 0.7692308 0.3571429 0.4000000 0.6250000 10.3997185 0.0000000
#> CTNNB1 1.4545455 0.0000000 2.7692308 0.0000000 0.0000000 11.3006993
#> EGFR 2.3225806 0.3225806 1.3942308 2.3225806 0.6166983 2.0000000
#> KEAP1 1.7692308 0.0000000 1.0000000 0.7692308 0.0000000 1.0000000
#> KRAS 4.2500000 10.7706044 0.9821429 2.3942308 3.7335165 0.7692308
#> MGA 1.7692308 0.0000000 2.7513736 0.0000000 0.6512605 0.0000000
#> NF1 0.6250000 1.3942308 1.1513158 0.6250000 0.0000000 0.0000000
#> PIK3CA 0.0000000 0.0000000 2.6250000 1.0000000 0.0000000 0.0000000
#> PTPRD 0.3225806 0.3225806 1.6250000 1.4021261 0.9475806 0.0000000
#> PTPRT 1.6250000 0.7692308 0.4000000 0.6250000 0.6250000 0.0000000
#> RB1 0.7692308 0.0000000 1.1513158 0.0000000 0.7692308 0.0000000
#> RBM10 0.0000000 1.0000000 2.7692308 1.3942308 0.9821429 1.5384615
#> SETBP1 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000
#> SETD2 2.0000000 0.0000000 4.5263158 0.0000000 0.0000000 1.0000000
#> SMAD4 2.1692308 0.0000000 1.2500000 1.0250000 0.6250000 0.0000000
#> SMARCA4 0.4545455 0.7692308 0.4000000 1.0795455 0.0000000 0.4545455
#> STK11 0.7692308 6.5384615 1.3942308 1.9930070 0.0000000 1.0000000
#> TP53 5.3668114 1.6618664 13.1174667 8.6168114 4.7733449 1.7692308
#> U2AF1 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000
#> EGFR KEAP1 KRAS MGA NF1 PIK3CA
#> ARID1A 2.3225806 1.7692308 4.2500000 1.7692308 0.6250000 0.0000000
#> ATM 0.3225806 0.0000000 10.7706044 0.0000000 1.3942308 0.0000000
#> BRAF 1.3942308 1.0000000 0.9821429 2.7513736 1.1513158 2.6250000
#> CDKN2A 2.3225806 0.7692308 2.3942308 0.0000000 0.6250000 1.0000000
#> CMTR2 0.6166983 0.0000000 3.7335165 0.6512605 0.0000000 0.0000000
#> CTNNB1 2.0000000 1.0000000 0.7692308 0.0000000 0.0000000 0.0000000
#> EGFR 53.6412020 0.0000000 0.0000000 2.2941176 0.6250000 2.0000000
#> KEAP1 0.0000000 28.8257663 12.5384615 0.7692308 3.3942308 0.7692308
#> KRAS 0.0000000 12.5384615 129.2909446 2.5085165 3.2500000 3.3942308
#> MGA 2.2941176 0.7692308 2.5085165 17.3393316 0.0000000 0.4000000
#> NF1 0.6250000 3.3942308 3.2500000 0.0000000 25.6007085 0.7692308
#> PIK3CA 2.0000000 0.7692308 3.3942308 0.4000000 0.7692308 16.6474696
#> PTPRD 0.6451613 0.7692308 1.5384615 0.5263158 0.0000000 0.0000000
#> PTPRT 1.0000000 0.5263158 1.5384615 0.0000000 0.0000000 0.0000000
#> RB1 2.0000000 0.7692308 1.1513158 1.1513158 2.0000000 1.2500000
#> RBM10 3.7692308 1.0000000 13.9725275 1.3571429 1.1513158 0.0000000
#> SETBP1 0.0000000 0.7692308 2.5513158 0.8000000 0.6250000 0.0000000
#> SETD2 3.0000000 1.3571429 3.2955466 0.0000000 1.0000000 2.0000000
#> SMAD4 3.6250000 0.0000000 0.4545455 1.0000000 0.6250000 0.0000000
#> SMARCA4 0.0000000 2.1263736 1.7692308 0.0000000 0.6250000 0.7692308
#> STK11 0.0000000 9.3076923 25.9230769 2.5384615 3.0000000 0.6250000
#> TP53 29.3335097 7.2103817 35.8760174 7.1410957 17.1417004 8.1090081
#> U2AF1 0.0000000 0.0000000 5.3076923 0.0000000 0.7692308 0.0000000
#> PTPRD PTPRT RB1 RBM10 SETBP1 SETD2
#> ARID1A 0.3225806 1.6250000 0.7692308 0.0000000 0.0000000 2.0000000
#> ATM 0.3225806 0.7692308 0.0000000 1.0000000 0.0000000 0.0000000
#> BRAF 1.6250000 0.4000000 1.1513158 2.7692308 1.0000000 4.5263158
#> CDKN2A 1.4021261 0.6250000 0.0000000 1.3942308 0.0000000 0.0000000
#> CMTR2 0.9475806 0.6250000 0.7692308 0.9821429 0.0000000 0.0000000
#> CTNNB1 0.0000000 0.0000000 0.0000000 1.5384615 0.0000000 1.0000000
#> EGFR 0.6451613 1.0000000 2.0000000 3.7692308 0.0000000 3.0000000
#> KEAP1 0.7692308 0.5263158 0.7692308 1.0000000 0.7692308 1.3571429
#> KRAS 1.5384615 1.5384615 1.1513158 13.9725275 2.5513158 3.2955466
#> MGA 0.5263158 0.0000000 1.1513158 1.3571429 0.8000000 0.0000000
#> NF1 0.0000000 0.0000000 2.0000000 1.1513158 0.6250000 1.0000000
#> PIK3CA 0.0000000 0.0000000 1.2500000 0.0000000 0.0000000 2.0000000
#> PTPRD 8.4587148 1.8750000 0.0000000 1.0000000 0.0000000 0.0000000
#> PTPRT 1.8750000 9.1160931 0.0000000 0.5263158 0.0000000 0.5263158
#> RB1 0.0000000 0.0000000 14.6104159 0.0000000 0.0000000 0.5263158
#> RBM10 1.0000000 0.5263158 0.0000000 24.2078514 1.0000000 0.5263158
#> SETBP1 0.0000000 0.0000000 0.0000000 1.0000000 7.2546375 0.0000000
#> SETD2 0.0000000 0.5263158 0.5263158 0.5263158 0.0000000 18.7700983
#> SMAD4 1.2500000 0.6250000 0.0000000 0.0000000 0.0000000 2.0000000
#> SMARCA4 0.4545455 1.4000000 0.7692308 0.0000000 0.4545455 0.8834586
#> STK11 1.2237762 2.0000000 0.6250000 3.7692308 1.0000000 1.5384615
#> TP53 1.8951613 4.0718623 12.0045547 5.0840081 4.6296375 3.1790052
#> U2AF1 0.7692308 0.0000000 0.0000000 0.0000000 1.0000000 0.7692308
#> SMAD4 SMARCA4 STK11 TP53 U2AF1
#> ARID1A 2.1692308 0.4545455 0.7692308 5.366811 0.0000000
#> ATM 0.0000000 0.7692308 6.5384615 1.661866 0.0000000
#> BRAF 1.2500000 0.4000000 1.3942308 13.117467 1.0000000
#> CDKN2A 1.0250000 1.0795455 1.9930070 8.616811 0.0000000
#> CMTR2 0.6250000 0.0000000 0.0000000 4.773345 0.0000000
#> CTNNB1 0.0000000 0.4545455 1.0000000 1.769231 0.0000000
#> EGFR 3.6250000 0.0000000 0.0000000 29.333510 0.0000000
#> KEAP1 0.0000000 2.1263736 9.3076923 7.210382 0.0000000
#> KRAS 0.4545455 1.7692308 25.9230769 35.876017 5.3076923
#> MGA 1.0000000 0.0000000 2.5384615 7.141096 0.0000000
#> NF1 0.6250000 0.6250000 3.0000000 17.141700 0.7692308
#> PIK3CA 0.0000000 0.7692308 0.6250000 8.109008 0.0000000
#> PTPRD 1.2500000 0.4545455 1.2237762 1.895161 0.7692308
#> PTPRT 0.6250000 1.4000000 2.0000000 4.071862 0.0000000
#> RB1 0.0000000 0.7692308 0.6250000 12.004555 0.0000000
#> RBM10 0.0000000 0.0000000 3.7692308 5.084008 0.0000000
#> SETBP1 0.0000000 0.4545455 1.0000000 4.629637 1.0000000
#> SETD2 2.0000000 0.8834586 1.5384615 3.179005 0.7692308
#> SMAD4 11.4987762 0.0000000 0.0000000 4.104545 0.0000000
#> SMARCA4 0.0000000 15.8856578 2.0795455 8.342559 0.0000000
#> STK11 0.0000000 2.0795455 50.7886456 9.545639 0.0000000
#> TP53 4.1045455 8.3425588 9.5456386 165.851389 4.5384615
#> U2AF1 0.0000000 0.0000000 0.0000000 4.538462 10.6153846
#>
# }