\name{readParamsRFile} \alias{readParamsRFile} \title{Read cnvGSA parameters from a file (R format)} \description{ Reads cnvGSA parameters from a text file that has them encoded using R syntax. } \details{ To make it easier to integrate the association test into a larger bioinformatics pipeline, it is convenient to read in the parameters from an external source such as a text file. One such implementation is to record each parameter on its own line using R syntax: \code{ grandtotals_mode <- "all" sample_classes <- c("case", "ctrl") fdr_iter <- 1000 extended_report <- 200 boxplot_PDFs <- FALSE limits_type <- "DEL" } The package provides \code{readParamsRFile()} to parse such a file (essentially just source()ing it and then handling the few possibilites around the cnvData\$filters parameters). } \usage{ readParamsRFile(filename) } \arguments{ \item{filename}{Name of the file.} } \value{ Test parameters in a list structure that can be assigned to the \code{params} slot of a \code{CnvGSAInput} object. } \author{Robert Ziman \email{rziman@gmail.com}} \examples{ paramFile <- system.file("scripts", "params_example.R", package="cnvGSA") params <- readParamsRFile(paramFile) }