Shortcut for the main function to analyse negative binomial data
valid object defining a directed acyclic graph
data frame with wild type expression values
data from with mutation type expression values
additional arguments for the solver function
character string for the method to define the adjustment set Z for the regression
method of computing causal effects
character string. "mean", "sum" for standard summary functions, "hmp" for harmonic mean, "test" for the selfcontained test of package 'CombinePValue' or any method from package 'metap', e.g., "meanp" or "sump".
either "wald" for testing significance with the wald test or "lr" for using a likelihood ratio test
either a numeric vector of the same length as the sum of wild type and mutant samples or a logical. If TRUE, it is recommended that both data sets include not only the genes included in the graph but all genes available in the original data set.
indicates whether adjustment against latent confounding is used. If FALSE, no adjustment is used, if TRUE it adjusts for confounding by automatically estimating the number of latent confounders. The estimated number of latent confounders can be chosen manually by setting this variable to some number.
logical; if TRUE, does not use the indicator variable for the variables in the adjustment set
Control verbosity (logger::INFO, logger::DEBUG, ...)
list of matrices with dces and corresponding p-value
dag <- create_random_DAG(30, 0.2)
X.wt <- simulate_data(dag)
dag.mt <- resample_edge_weights(dag)
X.mt <- simulate_data(dag)
dce_nb(dag,X.wt,X.mt)
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#> Warning: glm.fit2: algorithm did not converge. Try increasing the maximum iterations
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#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: glm.fit2: algorithm did not converge. Try increasing the maximum iterations
#> Warning: alternation limit reached
#> Warning: glm.fit2: algorithm did not converge. Try increasing the maximum iterations
#> Warning: glm.fit2: algorithm did not converge. Try increasing the maximum iterations
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
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#> Warning: alternation limit reached
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#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: inner loop 3; cannot correct step size
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
#> Warning: step size truncated due to increasing deviance
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#> $graph
#> n1 n2 n3 n4 n5 n6 n7 n8 n9 n10 n11 n12 n13 n14 n15 n16 n17 n18 n19 n20 n21
#> n1 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1
#> n2 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 1 0 0 0 0
#> n3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
#> n4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1
#> n5 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0
#> n6 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0
#> n7 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
#> n8 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0
#> n9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
#> n10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
#> n11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
#> n12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n13 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
#> n14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
#> n15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
#> n17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
#> n18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
#> n21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> n22 n23 n24 n25 n26 n27 n28 n29 n30
#> n1 0 0 0 0 0 0 0 0 0
#> n2 1 0 0 0 0 0 0 0 0
#> n3 0 0 0 0 0 0 1 0 0
#> n4 0 0 0 0 0 0 0 0 0
#> n5 1 1 0 0 0 0 0 0 0
#> n6 0 1 0 0 0 0 0 1 0
#> n7 0 0 0 1 0 0 0 0 0
#> n8 0 0 0 0 0 0 0 0 0
#> n9 0 0 0 0 0 0 0 0 0
#> n10 0 0 0 0 0 1 0 0 0
#> n11 1 0 1 0 0 0 0 0 1
#> n12 0 0 0 0 1 0 0 0 0
#> n13 0 1 0 0 0 1 0 0 0
#> n14 0 0 0 0 0 0 0 0 0
#> n15 0 0 1 0 0 0 0 1 0
#> n16 0 0 0 0 0 0 1 0 0
#> n17 0 0 0 0 0 0 0 0 0
#> n18 0 0 0 1 0 0 0 0 0
#> n19 0 0 0 0 0 0 0 0 0
#> n20 0 0 1 0 0 0 0 1 0
#> n21 0 0 0 0 1 1 0 0 1
#> n22 0 0 0 0 1 0 0 0 0
#> n23 0 0 0 0 0 0 1 0 0
#> n24 0 0 0 0 0 0 0 0 0
#> n25 0 0 0 0 0 0 0 0 0
#> n26 0 0 0 0 0 0 0 0 1
#> n27 0 0 0 0 0 0 0 0 0
#> n28 0 0 0 0 0 0 0 0 0
#> n29 0 0 0 0 0 0 0 0 0
#> n30 0 0 0 0 0 0 0 0 0
#>
#> $dce
#> n1 n2 n3 n4 n5 n6 n7 n8 n9 n10
#> n1 NA NA NA 0.009598431 NA 0.003833928 0.00281002 NA NA NA
#> n2 NA NA NA NA NA NA NA -0.006351443 NA NA
#> n3 NA NA NA NA NA NA NA NA NA NA
#> n4 NA NA NA NA NA NA NA NA NA NA
#> n5 NA NA NA NA NA NA NA NA NA -0.001925493
#> n6 NA NA NA NA NA NA NA -0.069200051 NA NA
#> n7 NA NA NA NA NA NA NA NA NA NA
#> n8 NA NA NA NA NA NA NA NA NA NA
#> n9 NA NA NA NA NA NA NA NA NA NA
#> n10 NA NA NA NA NA NA NA NA NA NA
#> n11 NA NA NA NA NA NA NA NA NA NA
#> n12 NA NA NA NA NA NA NA NA NA NA
#> n13 NA NA NA NA NA NA NA NA NA NA
#> n14 NA NA NA NA NA NA NA NA NA NA
#> n15 NA NA NA NA NA NA NA NA NA NA
#> n16 NA NA NA NA NA NA NA NA NA NA
#> n17 NA NA NA NA NA NA NA NA NA NA
#> n18 NA NA NA NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA NA NA NA
#> n20 NA NA NA NA NA NA NA NA NA NA
#> n21 NA NA NA NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA NA NA NA
#> n11 n12 n13 n14 n15 n16 n17
#> n1 NA NA NA NA NA NA 0.15264860
#> n2 NA -0.001201424 NA 0.37218517 NA NA 0.02852566
#> n3 -0.1042891 NA NA NA NA NA NA
#> n4 NA NA NA NA NA NA -0.11754459
#> n5 NA NA NA NA NA -0.5356231 NA
#> n6 NA NA NA NA NA -0.3470092 NA
#> n7 -0.8510483 NA NA NA NA NA NA
#> n8 NA 0.133898536 NA NA NA NA NA
#> n9 NA NA NA NA NA NA NA
#> n10 NA NA NA NA NA NA NA
#> n11 NA NA NA NA NA -0.1959073 NA
#> n12 NA NA NA NA NA NA NA
#> n13 NA NA NA 0.01825183 -0.004013498 NA NA
#> n14 NA NA NA NA 0.010352180 NA NA
#> n15 NA NA NA NA NA NA NA
#> n16 NA NA NA NA NA NA NA
#> n17 NA NA NA NA NA NA NA
#> n18 NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA
#> n20 NA NA NA NA NA NA NA
#> n21 NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA
#> n18 n19 n20 n21 n22 n23 n24
#> n1 NA NA NA 0.1964665 NA NA NA
#> n2 NA NA NA NA 0.128929749 NA NA
#> n3 NA NA NA NA NA NA NA
#> n4 NA NA NA 0.1151990 NA NA NA
#> n5 NA 0.2043502 NA NA 0.003705346 0.1325395 NA
#> n6 NA NA NA NA NA -0.4332542 NA
#> n7 NA NA NA NA NA NA NA
#> n8 NA 1.8243552 NA NA NA NA NA
#> n9 NA NA -0.05508431 NA NA NA NA
#> n10 NA 0.3941495 NA NA NA NA NA
#> n11 NA NA NA NA -0.563550381 NA -0.8216571
#> n12 NA NA NA NA NA NA NA
#> n13 NA NA NA NA NA -0.1758228 NA
#> n14 NA NA NA NA NA NA NA
#> n15 NA NA NA NA NA NA -1.1836663
#> n16 NA NA 0.37730613 NA NA NA NA
#> n17 NA NA -1.15635476 NA NA NA NA
#> n18 NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA
#> n20 NA NA NA 0.9508950 NA NA -0.4145703
#> n21 NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA
#> n25 n26 n27 n28 n29 n30
#> n1 NA NA NA NA NA NA
#> n2 NA NA NA NA NA NA
#> n3 NA NA NA -0.01000148 NA NA
#> n4 NA NA NA NA NA NA
#> n5 NA NA NA NA NA NA
#> n6 NA NA NA NA 0.12422530 NA
#> n7 0.1333317 NA NA NA NA NA
#> n8 NA NA NA NA NA NA
#> n9 NA NA NA NA NA NA
#> n10 NA NA 0.1265809 NA NA NA
#> n11 NA NA NA NA NA -0.17385888
#> n12 NA -0.2658790 NA NA NA NA
#> n13 NA NA 0.4434459 NA NA NA
#> n14 NA NA NA NA NA NA
#> n15 NA NA NA NA -2.36419723 NA
#> n16 NA NA NA 0.29425915 NA NA
#> n17 NA NA NA NA NA NA
#> n18 -0.1851477 NA NA NA NA NA
#> n19 NA NA NA NA NA NA
#> n20 NA NA NA NA 0.03254787 NA
#> n21 NA -0.3219329 1.4830725 NA NA 0.28747208
#> n22 NA 0.3983095 NA NA NA NA
#> n23 NA NA NA -1.00736809 NA NA
#> n24 NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA
#> n26 NA NA NA NA NA -0.08511788
#> n27 NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA
#>
#> $dce_stderr
#> n1 n2 n3 n4 n5 n6 n7 n8 n9 n10
#> n1 NA NA NA 0.008863754 NA 0.009760324 0.008747657 NA NA NA
#> n2 NA NA NA NA NA NA NA 0.01415069 NA NA
#> n3 NA NA NA NA NA NA NA NA NA NA
#> n4 NA NA NA NA NA NA NA NA NA NA
#> n5 NA NA NA NA NA NA NA NA NA 0.008069067
#> n6 NA NA NA NA NA NA NA 0.25378572 NA NA
#> n7 NA NA NA NA NA NA NA NA NA NA
#> n8 NA NA NA NA NA NA NA NA NA NA
#> n9 NA NA NA NA NA NA NA NA NA NA
#> n10 NA NA NA NA NA NA NA NA NA NA
#> n11 NA NA NA NA NA NA NA NA NA NA
#> n12 NA NA NA NA NA NA NA NA NA NA
#> n13 NA NA NA NA NA NA NA NA NA NA
#> n14 NA NA NA NA NA NA NA NA NA NA
#> n15 NA NA NA NA NA NA NA NA NA NA
#> n16 NA NA NA NA NA NA NA NA NA NA
#> n17 NA NA NA NA NA NA NA NA NA NA
#> n18 NA NA NA NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA NA NA NA
#> n20 NA NA NA NA NA NA NA NA NA NA
#> n21 NA NA NA NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA NA NA NA
#> n11 n12 n13 n14 n15 n16 n17 n18
#> n1 NA NA NA NA NA NA 0.12834634 NA
#> n2 NA 0.009389227 NA 0.05440526 NA NA 0.01182577 NA
#> n3 0.02382006 NA NA NA NA NA NA NA
#> n4 NA NA NA NA NA NA 1.46803703 NA
#> n5 NA NA NA NA NA 0.1591343 NA NA
#> n6 NA NA NA NA NA 1.3252605 NA NA
#> n7 0.72634330 NA NA NA NA NA NA NA
#> n8 NA 0.228317702 NA NA NA NA NA NA
#> n9 NA NA NA NA NA NA NA NA
#> n10 NA NA NA NA NA NA NA NA
#> n11 NA NA NA NA NA 1.3759610 NA NA
#> n12 NA NA NA NA NA NA NA NA
#> n13 NA NA NA 0.14649229 0.005847307 NA NA NA
#> n14 NA NA NA NA 0.044609583 NA NA NA
#> n15 NA NA NA NA NA NA NA NA
#> n16 NA NA NA NA NA NA NA NA
#> n17 NA NA NA NA NA NA NA NA
#> n18 NA NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA NA
#> n20 NA NA NA NA NA NA NA NA
#> n21 NA NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA NA
#> n19 n20 n21 n22 n23 n24 n25
#> n1 NA NA 0.03582602 NA NA NA NA
#> n2 NA NA NA 0.07056366 NA NA NA
#> n3 NA NA NA NA NA NA NA
#> n4 NA NA 0.57085925 NA NA NA NA
#> n5 0.01458461 NA NA 0.07203955 0.05642308 NA NA
#> n6 NA NA NA NA 1.34168624 NA NA
#> n7 NA NA NA NA NA NA 0.97935535
#> n8 2.84129847 NA NA NA NA NA NA
#> n9 NA 0.2197302 NA NA NA NA NA
#> n10 0.22487309 NA NA NA NA NA NA
#> n11 NA NA NA 0.50861416 NA 0.6763962 NA
#> n12 NA NA NA NA NA NA NA
#> n13 NA NA NA NA 0.20483030 NA NA
#> n14 NA NA NA NA NA NA NA
#> n15 NA NA NA NA NA 1.6288884 NA
#> n16 NA 1.2092014 NA NA NA NA NA
#> n17 NA 1.2904043 NA NA NA NA NA
#> n18 NA NA NA NA NA NA 0.02419575
#> n19 NA NA NA NA NA NA NA
#> n20 NA NA 0.68834842 NA NA 0.2392031 NA
#> n21 NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA
#> n26 n27 n28 n29 n30
#> n1 NA NA NA NA NA
#> n2 NA NA NA NA NA
#> n3 NA NA 0.07873164 NA NA
#> n4 NA NA NA NA NA
#> n5 NA NA NA NA NA
#> n6 NA NA NA 0.57403034 NA
#> n7 NA NA NA NA NA
#> n8 NA NA NA NA NA
#> n9 NA NA NA NA NA
#> n10 NA 1.7361622 NA NA NA
#> n11 NA NA NA NA 0.22495834
#> n12 0.4799656 NA NA NA NA
#> n13 NA 0.1692339 NA NA NA
#> n14 NA NA NA NA NA
#> n15 NA NA NA 1.71847662 NA
#> n16 NA NA 0.25576850 NA NA
#> n17 NA NA NA NA NA
#> n18 NA NA NA NA NA
#> n19 NA NA NA NA NA
#> n20 NA NA NA 0.09404295 NA
#> n21 0.5863109 1.2939338 NA NA 0.15464222
#> n22 0.1898496 NA NA NA NA
#> n23 NA NA 0.52474749 NA NA
#> n24 NA NA NA NA NA
#> n25 NA NA NA NA NA
#> n26 NA NA NA NA 0.08704132
#> n27 NA NA NA NA NA
#> n28 NA NA NA NA NA
#> n29 NA NA NA NA NA
#> n30 NA NA NA NA NA
#>
#> $dce_pvalue
#> n1 n2 n3 n4 n5 n6 n7 n8 n9 n10
#> n1 NA NA NA 0.2788592 NA 0.6944617 0.7480352 NA NA NA
#> n2 NA NA NA NA NA NA NA 0.6535448 NA NA
#> n3 NA NA NA NA NA NA NA NA NA NA
#> n4 NA NA NA NA NA NA NA NA NA NA
#> n5 NA NA NA NA NA NA NA NA NA 0.8113953
#> n6 NA NA NA NA NA NA NA 0.7851060 NA NA
#> n7 NA NA NA NA NA NA NA NA NA NA
#> n8 NA NA NA NA NA NA NA NA NA NA
#> n9 NA NA NA NA NA NA NA NA NA NA
#> n10 NA NA NA NA NA NA NA NA NA NA
#> n11 NA NA NA NA NA NA NA NA NA NA
#> n12 NA NA NA NA NA NA NA NA NA NA
#> n13 NA NA NA NA NA NA NA NA NA NA
#> n14 NA NA NA NA NA NA NA NA NA NA
#> n15 NA NA NA NA NA NA NA NA NA NA
#> n16 NA NA NA NA NA NA NA NA NA NA
#> n17 NA NA NA NA NA NA NA NA NA NA
#> n18 NA NA NA NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA NA NA NA
#> n20 NA NA NA NA NA NA NA NA NA NA
#> n21 NA NA NA NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA NA NA NA
#> n11 n12 n13 n14 n15 n16 n17
#> n1 NA NA NA NA NA NA 0.23430235
#> n2 NA 0.8981824 NA 7.865415e-12 NA NA 0.01585826
#> n3 1.196618e-05 NA NA NA NA NA NA
#> n4 NA NA NA NA NA NA 0.93618220
#> n5 NA NA NA NA NA 0.0007630678 NA
#> n6 NA NA NA NA NA 0.7934430581 NA
#> n7 2.413221e-01 NA NA NA NA NA NA
#> n8 NA 0.5575684 NA NA NA NA NA
#> n9 NA NA NA NA NA NA NA
#> n10 NA NA NA NA NA NA NA
#> n11 NA NA NA NA NA 0.8867810082 NA
#> n12 NA NA NA NA NA NA NA
#> n13 NA NA NA 9.008462e-01 0.4924709 NA NA
#> n14 NA NA NA NA 0.8164900 NA NA
#> n15 NA NA NA NA NA NA NA
#> n16 NA NA NA NA NA NA NA
#> n17 NA NA NA NA NA NA NA
#> n18 NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA
#> n20 NA NA NA NA NA NA NA
#> n21 NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA
#> n18 n19 n20 n21 n22 n23 n24
#> n1 NA NA NA 4.160395e-08 NA NA NA
#> n2 NA NA NA NA 0.06767859 NA NA
#> n3 NA NA NA NA NA NA NA
#> n4 NA NA NA 8.400736e-01 NA NA NA
#> n5 NA 1.328450e-44 NA NA 0.95897899 0.01882235 NA
#> n6 NA NA NA NA NA 0.74675761 NA
#> n7 NA NA NA NA NA NA NA
#> n8 NA 5.208180e-01 NA NA NA NA NA
#> n9 NA NA 0.8020533 NA NA NA NA
#> n10 NA 7.964248e-02 NA NA NA NA NA
#> n11 NA NA NA NA 0.26785681 NA 0.22445876
#> n12 NA NA NA NA NA NA NA
#> n13 NA NA NA NA NA 0.39068101 NA
#> n14 NA NA NA NA NA NA NA
#> n15 NA NA NA NA NA NA 0.46742739
#> n16 NA NA 0.7550183 NA NA NA NA
#> n17 NA NA 0.3701897 NA NA NA NA
#> n18 NA NA NA NA NA NA NA
#> n19 NA NA NA NA NA NA NA
#> n20 NA NA NA 1.671513e-01 NA NA 0.08307242
#> n21 NA NA NA NA NA NA NA
#> n22 NA NA NA NA NA NA NA
#> n23 NA NA NA NA NA NA NA
#> n24 NA NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA NA
#> n26 NA NA NA NA NA NA NA
#> n27 NA NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA NA
#> n25 n26 n27 n28 n29 n30
#> n1 NA NA NA NA NA NA
#> n2 NA NA NA NA NA NA
#> n3 NA NA NA 0.89891468 NA NA
#> n4 NA NA NA NA NA NA
#> n5 NA NA NA NA NA NA
#> n6 NA NA NA NA 0.8286690 NA
#> n7 8.917088e-01 NA NA NA NA NA
#> n8 NA NA NA NA NA NA
#> n9 NA NA NA NA NA NA
#> n10 NA NA 0.941878969 NA NA NA
#> n11 NA NA NA NA NA 0.43961161
#> n12 NA 0.57961011 NA NA NA NA
#> n13 NA NA 0.008784912 NA NA NA
#> n14 NA NA NA NA NA NA
#> n15 NA NA NA NA 0.1688985 NA
#> n16 NA NA NA 0.24994202 NA NA
#> n17 NA NA NA NA NA NA
#> n18 1.977594e-14 NA NA NA NA NA
#> n19 NA NA NA NA NA NA
#> n20 NA NA NA NA 0.7292707 NA
#> n21 NA 0.58294907 0.251723432 NA NA 0.06303429
#> n22 NA 0.03590276 NA NA NA NA
#> n23 NA NA NA 0.05489332 NA NA
#> n24 NA NA NA NA NA NA
#> n25 NA NA NA NA NA NA
#> n26 NA NA NA NA NA 0.32812282
#> n27 NA NA NA NA NA NA
#> n28 NA NA NA NA NA NA
#> n29 NA NA NA NA NA NA
#> n30 NA NA NA NA NA NA
#>
#> $pathway_pvalue
#> [1] 7.306473e-43
#>
#> $deconfounding
#> [1] FALSE
#>
#> attr(,"class")
#> [1] "dce"