Method for objects of class LowMACA. It can show the most important user-definable parameters for a LowMACA analysis and allows to change them.
an object of class LowMaca
a named list containing:
LowMACA is a suite of tool that analyze conserved mutations,
so it looks for clusters of gain of function alterations.
With 'missense' mutation_type we intend all those mutations that change
the original DNA but do not create stop codon nor alter the reading frame
(these mutations are collectively defined as 'truncating' mutations).
In addition we let the possibility to also choose 'silent' mutations
even though they are currently not supported by the cBioPortal.
To see all the available tumor types to run a LowMACA analysis, simply run
density_bw has a strong effect on the statistical analysis of LowMACA. With the default bandwidth (0),
the Shannon entropy calculation becomes descrete, while the continuos version is used in all the other cases.
lmParams is used as a show method it returns a named list of 5 elements:
Stefano de Pretis , Giorgio Melloni
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#Construct a LowMACA object lm <- newLowMACA(pfam="PF12906") #Show default parameters lmParams(lm) #Change all parameters lmParams(lm) <- list(mutation_type='all' , tumor_type=c('skcm','brca') , min_mutation_number=0 , density_bw=0 , clustal_cmd='clustalo' , use_hmm=FALSE , datum=FALSE) #Change just one parameter lmParams(lm)[['tumor_type']] <- 'prad'
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