parameterPreprocess: Preprocess Pipeline Parameter List.

In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

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 [e-mail]

See Also

See vignettes: browseVignettes("ramwas").

Examples

param = ramwasParameters(
    dirproject = "."
)

param2 = parameterPreprocess(param)

print(param2)

andreyshabalin/ramwas documentation built on Sept. 27, 2021, 7:25 p.m.