#getPrevalence<-function(lambda_S,mu_S,major_cn,minor_cn, lambda_G=NULL, mu_G=NULL, detail=0, mode="PhasedSNP",Trace=FALSE )
#mode="FlankingSNP"
#mode="PhasedSNP"
#Trace=T
lambda_S=lambda_somatic
mu_S=mu_somatic
lambda_G=lambda_LinkedGermline
mu_G=mu_LinkedGermline
{
N=length(lambda_S) # Number of samples
if((length(mu_S)!=N) ||
(!is.null(lambda_G) && ((length(lambda_G) !=N) || (length(mu_G) !=N))) ||
(length(major_cn) !=N) || (length(minor_cn)!=N) )
stop("\n\nThe vectors passed as input should have the same size\n\n")
if(mode=="PhasedSNP"){
prev_somatic=getPhasedSNPPrevalence( lambda_S,mu_S , major_cn,minor_cn, lambda_G , mu_G,detail,Trace=Trace )
}else if(mode=="FlankingSNP"){
prev_somatic=getFlankingSNPPrevalence( lambda_S,mu_S , major_cn,minor_cn,lambda_G , mu_G, detail,Trace=Trace)
}else if(mode=="SNVOnly"){
prev_somatic=getSNVOnlyPrevalence(lambda_S,mu_S ,major_cn,minor_cn, detail, Trace=Trace )
}else {
stop("parameter mode should be either FlankingCNP, PhasedSNP or SNVOnly")
}
prev_somatic
}
print(prev_somatic)
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