| IntsctEdg2Fw {EGRNi} | R Documentation |
To compute F score for significant edges from individual methods
Description
IntsctEdg2Fw computes the Fw score using Fisher's weighted method for the significant edges obtained in k numbers of individual methods. The probability values are combined to compute the Fw score which follows chi-square distribution. The significant edges (>fdr) are selected using intersection.
Usage
IntsctEdg2Fw(s, w, k, fdr)
Arguments
s |
Matrix containing edge scores obtained from k numbers of methods with gene pairs in row and edge scores in column |
w |
Matrix containing weight for all individual methods |
k |
Numbers of independent methods considered for computing edge scores |
fdr |
Cut-off for selecting significant edges |
Details
IntsctEdg2Fw function generates mixture distribution based on edge score for each method given column wise in s matrix. The probability value for each pair of gene obtained from mixture distribution are combined using Fisher's weighted method. The combined score Fw follows chi-square distribution with 2k degrees of freedom.
Value
Fw matrix containing F score for significant gene pairs
Author(s)
Chiranjib Sarkar(cschiranjib9@gmail.com)
References
Sarkar, C., Parsad, R., Mishra, D.C. and Rai, A. (2020). An ensemble approach for gene regulatory network study in rice blast. Journal of Crop and Weed , 16 , 1-8.
Examples
#load "EGRNi" library and Edge score data
library(EGRNi)
data(Edgescore)
data(weight)
IntsctEdg2Fw(Edgescore,weight, k=4, fdr=0.1)