MRPC (version 3.1.0)

data_with_outliers: Example data with outliers

Description

The data contain two genotype nodes, V1 and V2, and three phenotype nodes, T1, T2 and T3. The genotype nodes are discrete, whereas the phenotype nodes are continuous. The data matrix includes 10 outliers (noises) generated from a uniform distribution. The example code below compares the performance of MRPC, pc, pc.stable, mmpc, mmhc, and hc on this data set.

Value

Matrix

Examples

# NOT RUN {
  
# }
# NOT RUN {
# Load packages

library(MRPC)     # MRPC
library(pcalg)    # pc
library(bnlearn)  # pc.stable, mmpc, mmhc, and hc


# Truth without outlier
tarmat <- matrix(0,
                 nrow = ncol(data_with_outliers),
                 ncol = ncol(data_with_outliers))
colnames(tarmat) <- colnames(data_with_outliers)
rownames(tarmat) <- colnames(data_with_outliers)

tarmat[1,2] <- 1
tarmat[2,1] <- 1
tarmat[1,3] <- 1
tarmat[4,3] <- 1
tarmat[4,5] <- 1

# Graph
Truth <- as(tarmat,
            "graphNEL")

# Data without outliers
n <- nrow(data_without_outliers)     # Number of rows
V <- colnames(data_without_outliers) # Column names

# Calculate Pearson correlation
suffStat_C1 <- list(C = cor(data_without_outliers),
                    n = n)

# Infer the graph by MRPC
MRPC.fit_withoutoutliers <- MRPC (data_without_outliers, 
                                  suffStat = suffStat_C1, 
                                  GV = 2, 
                                  FDR = 0.05, 
                                  indepTest ='gaussCItest', 
                                  labels = V, 
                                  FDRcontrol = 'LOND', 
                                  verbose = FALSE)

# Infer the graph by pc 
pc.fit_withoutoutliers <- pc(suffStat = suffStat_C1,
                            indepTest = gaussCItest,
                            alpha = 0.05, 
                            labels = V,
                            verbose = FALSE)

# arcs not to be included from gene expression to genotype for blacklist argument 
# in pc.stable and mmpc

GV <- 2
to <- rep (colnames (data_without_outliers)[1:GV], each = (ncol (data_without_outliers) - GV))
from <- rep (colnames (data_without_outliers)[(GV + 1):ncol (data_without_outliers)], GV)
bl <- cbind (from, to)

# Infer the graph by pc.stable
pc.stable_withoutoutliers <- pc.stable (data.frame (data_without_outliers), 
                                        blacklist = bl, 
                                        alpha = 0.05, 
                                        debug = FALSE, 
                                        undirected = FALSE)
# Infer the graph by mmpc
mmpc_withoutoutliers <- mmpc (data.frame (data_without_outliers), 
                              blacklist = bl, 
                              alpha = 0.05, 
                              debug = FALSE, 
                              undirected = FALSE)
# Infer the graph by mmhc
mmhc_withoutoutliers <- mmhc (data.frame (data_without_outliers), 
                              blacklist = bl, 
                              debug = FALSE)
# Infer the graph by hc
hc_withoutoutliers <- hc (data.frame (data_without_outliers), 
                          blacklist = bl, 
                          debug = FALSE)


# Data with outliers
n <- nrow (data_with_outliers)    # Number of rows
V <- colnames(data_with_outliers) # Column names

# Calculate Pearson correlation
suffStat_C2 <- list (C = cor (data_with_outliers), 
                     n = n)

# Infer the graph by MRPC
MRPC.fit_withoutliers_C2 <- MRPC (data_with_outliers, 
                                  suffStat = suffStat_C2, 
                                  GV = 2, 
                                  FDR = 0.05, 
                                  indepTest ='gaussCItest', 
                                  labels = V, 
                                  FDRcontrol = 'LOND', 
                                  verbose = FALSE)

# Infer the graph by pc
pc.fit_withoutliers_C2 <- pc (suffStat = suffStat_C2, 
                              indepTest = gaussCItest, 
                              alpha = 0.05, 
                              labels = V, 
                              verbose = FALSE)

# arcs not to be included from gene expression to genotype for blacklist argument 
# in pc.stable and mmpc

GV <- 2
to <- rep (colnames (data_with_outliers)[1:GV], each = (ncol (data_with_outliers) - GV))
from <- rep (colnames (data_with_outliers)[(GV + 1):ncol (data_with_outliers)], GV)
bl <- cbind (from, to)

# Infer the graph by pc.stable
pc.stable_withoutliers_C2 <- pc.stable (data.frame (data_with_outliers), 
                                        blacklist = bl, 
                                        alpha = 0.05, 
                                        B = NULL, 
                                        max.sx = NULL, 
                                        debug = FALSE, 
                                        undirected = FALSE)
# Infer the graph by mmpc
mmpc_withoutliers_C2 <- mmpc (data.frame (data_with_outliers), 
                              blacklist = bl, 
                              alpha = 0.05, 
                              B = NULL, 
                              max.sx = NULL, 
                              debug = FALSE, 
                              undirected = FALSE)
# Infer the graph by mmhc
mmhc_withoutliers_C2 <- mmhc (data.frame (data_with_outliers), 
                              blacklist = bl, 
                              debug = FALSE)


# Infer the graph by hc
hc_withoutliers_C2 <- hc (data.frame (data_with_outliers), 
                          blacklist = bl, 
                          debug = FALSE)

# Calculate robust correlation (Beta = 0.005)
Rcor_R1 <- RobustCor (data_with_outliers, 0.005)
suffStat_R1 <- list (C = Rcor_R1$RR, 
                     n = n)

# Infer the graph by MRPC with robust correlation
MRPC.fit_withoutliers_R1 <- MRPC (data_with_outliers, 
                                  suffStat = suffStat_R1, 
                                  GV = 2, 
                                  FDR = 0.05, 
                                  indepTest = 'gaussCItest', 
                                  labels = V, 
                                  FDRcontrol = 'LOND', 
                                  verbose = FALSE)

# Infer the graph by pc with robust correlation
pc.fit_withoutliers_R1 <- pc (suffStat = suffStat_R1, 
                              indepTest = gaussCItest, 
                              alpha = 0.05, 
                              labels = V, 
                              verbose = FALSE)


# True graph
plot (Truth, main = "Truth")

#-------------
# Plot inferred graphs
par (mfrow = c (2,6))

# Data without outliers
# Inference with Pearson correlation
plot (MRPC.fit_withoutoutliers, main = "MRPC")
plot (pc.fit_withoutoutliers, main = "pc")
graphviz.plot (pc.stable_withoutoutliers, main = "pc.stable")
graphviz.plot (mmpc_withoutoutliers, main = "mmpc")
graphviz.plot (mmhc_withoutoutliers, main = "mmhc")
graphviz.plot (hc_withoutoutliers, main = "hc")


# Data with outliers
# Inference with Pearson correlation
plot (MRPC.fit_withoutliers_C2, main = " ")
plot (pc.fit_withoutliers_C2, main = " ")
graphviz.plot (pc.stable_withoutliers_C2, main = " ")
graphviz.plot (mmpc_withoutliers_C2, main = " ")
graphviz.plot (mmhc_withoutliers_C2, main = " ")
graphviz.plot (hc_withoutliers_C2, main = " ")

#-------------
# Data with outliers
# Inference with robust correlation
par (mfrow = c (1,2))
plot (MRPC.fit_withoutliers_R1, main = "MRPC")
plot (pc.fit_withoutliers_R1, main = "pc")

# }
# NOT RUN {
  
# }