How to get the adjacency matrix of genes

[Salmi9]

How to get the adjacency matrix of genes

[zty2009]

gene-net1.txt is a matrix and its dimension is 6782*6782, which means interaction between any two genes is recorded in this file.
To obtain a file like this:

1. download gene interactions data (eg.GI.txt ) from Humannet v2.0.
2. select the genes you are interested in from GI.txt and build a new file.
   The format of the new file should like this:
   EntrezGeneID1 EntrezGeneID2 interaction_score
   10054 10055 5.05335388993672
   116150 79947 5.05271998874105
   23399 255919 5.04390232648848
   2339 2342 5.04149870387255
   6389 6390 5.04008076384162
   5432 5439 5.02733989558101
   593 594 5.02134747384889
3. If the number of genes you are interested in is N, you can build a N*N matrix. Each column and row is the list of genes.
4. fill the matrix with the new file in step 2.
5. Normalized this matrix.

[Salmi9]

Thanks for your prompt reply, do you need to fill it manually in the fourth step or is there any code that can be implemented?

[zty2009]

You need to write a two-layer ‘for’ loop.

[Salmi9]

Can you provide the program code? I would be very grateful, if it is not convenient, forget it.

[zty2009]

This is a demo of the code. You can try to fix it to work in your project.

library(data.table)

GI_new=fread('GI_new.txt',stringsAsFactor=F,data.table=F)
allgene=fread('allgene.txt',stringsAsFactor=F,data.table=F) ##genes you are interested in

A=matrix(0,nrow(allgene),nrow(allgene))

for (i in 1:nrow(allgene)){
for (j in i:nrow(allgene)){
index1=which(GI_new[,1]==allgene[i,1])
index2=which(GI_new[,2]==allgene[j,1])
index=intersect(index1,index2)
if (length(index)==0){
index1=which(GI_new[,2]==allgene[i,1])
index2=which(GI_new[,1]==allgene[j,1])
index=intersect(index1,index2)
}

if (length(index)!=0){
	
	A[i,j]=GI_new[index,3]
	A[j,i]=GI_new[index,3]
}

}

}

[Salmi9]

Thanks so much for your enthusiastic help, which solved one of my difficulties！