parameterPreprocess {ramwas} | R Documentation |
Fill in missing parameters with default values, read supporting data files, make relative directory path parameters absolute.
parameterPreprocess(param)
param |
List with RaMWAS parameters. |
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.
Returns preprocessed list of parameters.
This function is not intended to be run by the user.
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
.
param = ramwasParameters( dirproject = "." ) param2 = parameterPreprocess(param) print(param2)