Viper error while creating Regulon object from minet adjacency matrix file ?
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@prithvi146510-24286
Last seen 11 months ago

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

software error • 234 views
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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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