parallelize: Show and set parallelization options

In ste-depo/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Show and set parallelization options

Description

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

Usage

parallelize(object)
parallelize(object) <- value

Arguments

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

Details

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.

Value

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

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

getMutations

Examples

#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

ste-depo/LowMACA documentation built on Oct. 15, 2022, 11:53 p.m.