PC Algorithm with the Principle of Mendelian Randomization

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Documentation for package ‘MRPC’ version 3.1.0

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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