BiocManager::install("minet") BiocManager::install("aracne.networks") BiocManager::install("minet") BiocManager::install("Rgraphviz") BiocManager::install("viper") BiocManager::install("bcellViper") BiocManager::install("mixtools") library(bcellViper) library(mixtools) library(Rgraphviz) library(minet) library(aracne.networks) library(minet) library(viper)
rawCountTable <- read.delim(file.choose()) ####Choose your expression data#####
rawCountTable2 <- as.matrix(read.delim(file = "LUSCIRGs233.txt", header = TRUE, sep = "\t")) ###Same expression file as matrix format#####
MIS <- build.mim(rawCountTable, estimator = "spearman", disc = "none", nbins = sqrt(NROW(rawCountTable))) T1 <- minet(rawCountTable, method="aracne", estimator="spearman", disc="none", nbins=sqrt(NROW(rawCountTable))) regul <- aracne2regulon(T1, rawCountTable2, verbose = FALSE)
After running the last line i get the following error: Error in readLines(fname) : 'con' is not a connection
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I have created the weighted adjacency file using minet package in R by applying the aracne algorithm. Next I wish to perform master regulator analysis using viper R package. But for that i need to transform my adjacency matrix into a regulon object. While doing so with Viper, I'm encountering an error:
Install Packages
BiocManager::install("minet") BiocManager::install("aracne.networks") BiocManager::install("minet") BiocManager::install("Rgraphviz") BiocManager::install("viper") BiocManager::install("bcellViper") BiocManager::install("mixtools")
Run Packages
library(bcellViper) library(mixtools) library(Rgraphviz) library(minet) library(aracne.networks) library(minet) library(viper)
####Choose your expression data##### rawCountTable <- read.delim(file.choose())
Same expression file in matrix format
rawCountTable2 <- as.matrix(read.delim(file = "LUSCIRGs233.txt", header = TRUE, sep = "\t"))
Minet Package analysis
MIS <- build.mim(rawCountTable, estimator = "spearman", disc = "none", nbins = sqrt(NROW(rawCountTable))) T1 <- minet(rawCountTable, method="aracne", estimator="spearman", disc="none", nbins=sqrt(NROW(rawCountTable)))
Viper Regulon object creation
regul <- aracne2regulon(T1, rawCountTable2, verbose = FALSE)
After running the last line i get this error Error in readLines(fname) : 'con' is not a connection
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Did you ever find a solution to your problem? Ran into the same issue. Ram's input is not exactly helpful.