parameterPreprocess {ramwas} | R Documentation

## Preprocess Pipeline Parameter List.

### Description

Fill in missing parameters with default values, read supporting data files, make relative directory path parameters absolute.

### Usage

    parameterPreprocess(param)

### Arguments

`param` | List with RaMWAS parameters. For detailed description of all available parameters run: `browseVignettes("ramwas")`.

### Details

A number of common preprocessing steps necessary for parameters of multiple pipeline parts are combined in this function. The actions include

- Fill in default values for all missing parameters.

- Set bamnames parameter to the content filebamlist file (if bamnames was not set).

- Set bam2sample parameter to processed content of filebam2sample file (if bam2sample was not set).

- Set covariates parameter to the data frame from filecovariates file (if covariates was not set).

- Check parameters for consistency, i.e. that modelcovariates include only names of columns in covariates.

- Check that files filecpgset and filenoncpgset exist if the parameters are set.

### Value

Returns preprocessed list of parameters.

### Note

This function is not intended to be run by the user.

### Author(s)

Andrey A Shabalin andrey.shabalin@gmail.com

### See Also

See vignettes: `browseVignettes("ramwas")`.

### Examples

    param = ramwasParameters(
        dirproject = "."
    )

    param2 = parameterPreprocess(param)

    print(param2)

[Package ramwas version 1.4.0 Index]