getting adj matrix for minet package

Hi,

I have a matrix like below from a gold standard and I want to convert that to a symmetric adjacency matrix for using in minet package, how can do this please?

TFLocus    TargetLocus    InteractionType
AT5G10140    AT1G65480    -1
AT5G11260    AT1G27480    -1
AT5G11260    AT5G53370    -1
AT5G11260    AT1G03630    -1

gene r

• 1,169 views • link

updated 4.1 years ago by Ram

• written 10.7 years ago by zizigolu

0 answers

No answers yet.

More posts like this

How to make the SNP density plot using hapmap file
written 3.1 years ago by rj.rezwan •

Hi , have the Hapmap file `hapmap_file.hmp.txt` converted from `vcf`. I am trying to make a snp density plot like the given example. I want …
Making sublist of 26 gene lists
written 8.4 years ago by zizigolu

Hi, I have 26 lists of genes. I want to extract an overlap of 26 lists for clustering. something like below > head(inc[,1:4]) 31439_f_at 31440_at …
extracting multiple columns from a file
written 9.4 years ago by zizigolu

Hi, I have a file like below https://k52i.imgup.net/Untitled763f.jpg I want to extract rest of columns if in **gene column** we have `MYC`, `YY1` and `TP53` …
converting an edge list of genes to a full matrix(adjacency)
written 10.5 years ago by zizigolu

Hi I have an edge list derived from a gene regulatory network inferring algorithm like below ``` edge_list <- read.table("dream_GENIE3_predictions.txt", header = T, sep = …
removing and keeping some part of a matrix of genes interaction
written 10.6 years ago by zizigolu

Hi, I have a complete list of transcription factors in Arabidopsis thaliana like below ``` TF <- read.table("whole TF.txt", header = T, sep = "\t") …
removing gene-gene interaction from a correlation matrix
written 10.6 years ago by zizigolu

Hi, I have a list of transcription factors like below ``` TF <- read.table("whole TF.txt", header = T, sep = "\t") > View(TF) AGI_ID AT1G01010 …
converting a list of genes and interaction to a graph
written 10.6 years ago by zizigolu

Hi, I have a gold standard in Arabidopsis thaliana( genes and transcription factors and their interaction) like below ``` TFLocus TargetLocus InteractionType AT5G10140 AT1G65480 -1 …
changing a gold standard to a true network
written 10.6 years ago by zizigolu

I have a gold standard in Arabidopsis thaliana( genes and transcription factors) like below ``` TFLocus TargetLocus InteractionType AT5G10140 AT1G65480 -1 AT5G11260 AT1G27480 -1 AT5G11260 …
variance stabilization and normalization
written 10.7 years ago by zizigolu

Hi, I am going to perform variance stabilization on my data sets then I did like below ```r library(affy) library(vsn) celFiles <- list.celfiles() affyraw=ReadAffy(filenames = …
writing result from vsn package
written 10.7 years ago by zizigolu

Hi, I have 8 CEL files and I am going to perform variance stabilization on them. then I did like below ```r setwd("E:/Affy data") library(affy) …