BNrich: Analysis of significant final BNs

In Samaneh-Bioinformatics/BNrich: Pathway Enrichment Analysis Based on Bayesian Network

Description

Fisher's exact test applied to PEA on final BNs

Usage

BNrich(Ttest_Results, Pathway.id1, PathName_Final, fdr.value = 0.05)

Arguments

Ttest_Results	A data frame contains T-test results for all parameters
Pathway.id1	A vector contains modified KEEG pathway IDs
PathName_Final	A data frame contains is IDs and names of KEEG pathways
fdr.value	A numeric threshold to determine significant parameters

Value

A data frame contains fisher test results for any final pathways

Examples

#All the 187 preprocessed signaling pathways can be entered in analysis by fetch_data_file().
#But here you enter a subset of those pathways to see how this package works.
files <- system.file("extdata", "test_files_to_start.RData", package = "BNrich", mustWork = TRUE)
load(files)
Data <- system.file("extdata", "Test_DATA.RData", package = "BNrich", mustWork = TRUE)
load(Data)
uni_Result <- unify_path(dataH, dataD, MapkG = sub_mapkG, Pathway.id = path.id)
M1 <- uni_Result$mapkG1
BN <- BN_struct(M1)
data_h1 <- uni_Result$data_h
data_d1 <- uni_Result$data_d
LASSO_Result <- LASSO_BN(BN = BN , data_h = data_h1 , data_d = data_d1)
BN_h1 <- LASSO_Result$BN_h
BN_d1 <- LASSO_Result$BN_d
esti_result <- esti_par(BN_H = BN_h1, BN_D = BN_d1, data_h = data_h1, data_d = data_d1)
BNs_H <- esti_result$BNs_h
BNs_D <- esti_result$BNs_d
coef_h <- esti_result$coef_h
coef_d <- esti_result$coef_d
var_result <- var_mat(data_h1, coef_h,  BNs_H, data_d1, coef_d, BNs_D)
Var_H = var_result$var_mat_Bh
Var_D = var_result$var_mat_Bd
path.id1 <- uni_Result$pathway.id1
Ttest_result <- parm_Ttest(data_h1, coef_h, BNs_H, data_d1, coef_d, BNs_D, Var_H, Var_D, path.id1)
BNrich_result <- BNrich(Ttest_result, path.id1, Path.Name)

Samaneh-Bioinformatics/BNrich documentation built on April 6, 2020, 4:17 a.m.