readParamsRFile: Read cnvGSA parameters from a file (R format)

Description

Reads cnvGSA parameters from a text file that has them encoded using R syntax.

Usage

readParamsRFile(filename)

Arguments

filename

Name of the file.

Value

Test parameters in a list structure that can be assigned to the params slot of a CnvGSAInput object.

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:

grandtotals_mode <- "all" sample_classes <- c("case", "ctrl") fdr_iter <- 1000 extended_report <- 200 boxplot_PDFs <- FALSE limits_type <- "DEL"

The package provides readParamsRFile() to parse such a file (essentially just source()ing it and then handling the few possibilites around the cnvData\$filters parameters).

Examples

Run this code

paramFile <- system.file("scripts", "params_example.R", package="cnvGSA")
params <- readParamsRFile(paramFile)

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