AdjustMatrix |
Adjust the columns of the input matrix same as in the reference matrix |
aSHD |
Adjusted structural hamming distance (aSHD) |
CompareMethodsNodeOrdering |
Comparison of inference accuracy using the same data but with different node orderings. |
CompareMethodsVStructure |
Comparison of inference accuracy of different methods on data with and without a v-structure |
CutModules |
Cut a numeric variable into intervals |
data_examples |
Example data under simple and complex models |
data_GEUVADIS |
GEUVADIS data with 62 eQTL-gene sets |
data_GEUVADIS_combined |
Combined genotype and gene expression data from 62 eQTL-gene sets in 373 Europeans from GEUVADIS |
data_without_outliers |
Example data without outliers |
data_with_outliers |
Example data with outliers |
EdgeOrientation |
Perform edge orientation under the MRPC algorithm |
empty |
Check empty matrix |
IdentifyAssociatedPCs |
Identifyprincipal components (PCs) that are significantly associated with eQTLs and genes |
ModiSkeleton |
Infer a graph skeleton (undirected graph) |
mpinv |
Calculate the inverse matrix |
MRPC |
Infer a causal network using the MRPC algorithm |
MRPCclass-class |
Class of MRPC algorithm results |
MRPCtruth |
Graphs used as truth in simulation |
plot-method |
Class of MRPC algorithm results |
PlotDendrogram |
Plot a dendrogram and display node groups in colored modules |
PlotGraphWithModules |
Plot a graph with nodes in modules indicated by colors |
print.MRPCclass |
Class of MRPC algorithm results |
RecallPrecision |
Calculate recall and precision for two graphs |
RobustCor |
Calculate robust correlation matrix |
seqDiff |
Deviation between two graphs represented by two sequences |
SeqFDR |
Sequential FDR |
show-method |
Class of MRPC algorithm results |
SimulateData |
Simulate data under certain graphs |
SimulateData1P |
Simulate data for a node with one parent |
SimulateData2P |
Simulate data for a node with two parents |
SimulateData3P |
Simulate data for a node with three parents |
SimulateDataNP |
Simulate data for a node with no parent |
simu_data_layered |
Data for the layered model |
simu_data_M0 |
Data for Model 0 |
simu_data_M1 |
Data for Model 1 |
simu_data_M2 |
Data for Model 2 |
simu_data_M3 |
Data for Model 3 |
simu_data_M4 |
Data for Model 4 |
simu_data_multiparent |
Data for the multiple-parent model |
simu_data_starshaped |
Data for the star model |
summary-method |
Class of MRPC algorithm results |