Having trouble running run_viper (from DoRothEA)
The code I am running is posted below. Here "ec_results" is a file of type 'character'. Also, "ec_results" is the direct output of the toptable function.
library('dorothea')
library(bcellViper)
data(bcellViper, package = "bcellViper")
data(dorothea_hs, package = "dorothea")
tf_activities <- run_viper(ec_results, dorothea_hs)
The error I am getting is this:
Computing the association scores
Computing regulons enrichment with aREA
Error in wts^2: non-numeric argument to binary operator
Traceback:
1. run_viper(ec_results, dorothea_hs)
2. run_viper.data.frame(ec_results, dorothea_hs)
3. run_viper(as.matrix(input), regulons = regulons, options = options,
. tidy = tidy)
4. run_viper.matrix(as.matrix(input), regulons = regulons, options = options,
. tidy = tidy)
5. do.call(viper::viper, c(list(eset = input, regulon = .df2regulon(regulons)),
. options))
6. (function (eset, regulon, dnull = NULL, pleiotropy = FALSE, nes = TRUE,
. method = c("none", "scale", "rank", "mad", "ttest"), bootstraps = 0,
. minsize = 25, adaptive.size = FALSE, eset.filter = TRUE,
. mvws = 1, pleiotropyArgs = list(regulators = 0.05, shadow = 0.05,
. targets = 10, penalty = 20, method = "adaptive"), cores = 1,
. verbose = TRUE)
The error continues for multiple lines ~50 lines more.
Any help is appreciated! Thanks!
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