parallelize: Show and set parallelization options
In LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Description Usage Arguments Details Value Author(s) See Also Examples

Method for objects of class LowMACA. It can show parallelization parameters of an object of class LowMACA and switch off and on parallelization of alignSequences and getMutations method

1 2	parallelize(object) parallelize(object) <- value

`object`	object of class LowMaca
`value`	a named list containing logical values. Default list(getMutations=FALSE , makeAlignment=TRUE)

With getMutations=TRUE, the getMutations method runs in parallel during the queries to the different tumor_types. This can result in an overload to the cBioPortal database and the function returns error. With makeAlignment=TRUE, clustalo should run in parallel. Nevertheless, clustalo can be parallelized only if the OpenMP C library is correctly functioning.

If parallelize is used as a show method it returns a named list of two elements: getMutations and makeAlignment

Stefano de Pretis , Giorgio Melloni

getMutations

#Construct a LowMACA object
lm <- newLowMACA(pfam="PF12906")
#Show parallelize default
parallelize(lm)
#Change all parameters
parallelize(lm) <- list(getMutations=TRUE , makeAlignment=FALSE)
#Change just one parameter
parallelize(lm)[['getMutations']] <- TRUE