prepareBench.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/benchmarKIN-perturbation.R
\name{prepareBench}
\alias{prepareBench}
\title{prepareBench}
\usage{
prepareBench(act, meta, rm_bg = F, method_id = "method")
}
\arguments{
\item{act}{Activity matrix with kinases as rows and experiments as columns.}

\item{meta}{Data frame containing sample (experiment) information and perturb (target) in each experiment.}

\item{rm_bg}{Whether to remove experiments where no activity was inferred for the target kinase from the background set.}

\item{method_id}{ID for the method currently being tested.}
}
\value{
list of processed activity scores and meta data which can be used as direct input to the decoupler benchmark function
}
\description{
Prepares the input for the decoupler benchmark function.
}
\examples{
set.seed(123)

mat <- data.frame(exp1 = runif(5, min = -2, max = 2),
                  exp2 = runif(5, min = -3, max = 2))
rownames(mat) <- c("A", "B", "C", "D", "E")

meta <- data.frame(id = c("exp1", "exp2"),
                   target = c("A", "C"),
                   sign = c(1, -1))

out_list <- prepareBench(act = mat, meta = meta, method_id = "test")

}