R/updateParametersFromGenerics.R

In jperezrogers/rabbit: An R Package to Create Computational Pipelines to Develop and Evaluate Biomarkers from High Dimensional Genomic Data

# Function to update Task parameter list based on a list of generic variables
#
# Author: Joe Perez-Rogers
#
# @param parameters a list
# @param generics a list of generic variables
# @param module.class one of \code{M1}, \code{M2}, \code{M3}, or \code{M4}
#
# @return a \code{list} with the same names and dimensions as \code{parameters}
#
# @examples
# \dontrun{
# generics <- list(x = matrix(runif(100,2,15),nrow=10),
#                    y = rep(c(0,1),5))
# parameters <- list()
# module.class <- "M2"
#
# parameters <- updateParametersFromGenerics(parameters,generics,module.class)
# }
#
# @keywords internal

updateParametersFromGenerics <- function(parameters,generics,module.class){

  if(module.class=="M1"){

    parameters[["x"]] <- generics$x

    if("data"%in%names(parameters)){
      parameters[["data"]] <- generics$data
    }

  } else if(module.class=="M2"){

    parameters[["x"]] <- generics$x
    parameters[["y"]] <- generics$y

    if("data"%in%names(parameters)){
      parameters[["data"]] <- generics$data
    }

  } else if(module.class=="M3"){

    parameters[["x"]] <- generics$x
    parameters[["rank"]] <- generics$rank

  } else if(module.class=="M4"){

    parameters[["x"]] <- generics$x
    parameters[["y"]] <- generics$y

    if("data"%in%names(parameters)){
      parameters[["data"]] <- generics$data
    }

    parameters[["testdata"]] <- generics$testdata[row.names(generics$x),]

  }

  return(parameters)
}