Question: (Closed) Viper error while creating Regulon object ?
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gravatar for prithvi.mastermind
3 months ago by
prithvi.mastermind10 wrote:

I have created the wighted adjacency file using minet package by applying the aracne algorithm. Next i wish to perform master regulator analysis using viper R package. But for that i need a regulon object. I'm getting an error while making the regulon object.

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 = "LUSC_IRGs_233.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 this error

Error in readLines(fname) : 'con' is not a connection
ADD COMMENTlink modified 3 months ago by _r_am32k • written 3 months ago by prithvi.mastermind10

Hello prithvi.mastermind!

We believe that this post does not fit the main topic of this site.

Please ask https://support.bioconductor.org/ and format your post properly

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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Cheers!

ADD REPLYlink written 3 months ago by _r_am32k
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