Nothing
`input.checks.A` =
function(coef, phi, index, y, kappas, theta=FALSE, n=NULL, n0B=FALSE, trecase=FALSE){
classes = (unique(index))
f1 = c(1, 2, 5, 6)
if(!all(classes %in% 1:8)){
stop("index must be one of the predefined crosses: for AB, BA, AA, BB, for female or one sex model respectively 1, 2, 3, 4, for male mice in two sex model 5, 6, 7, 8")
}
nclasses = length(classes)
if((nclasses != 4) & (nclasses != 8)){
stop("model requires all 4 crosses for optimization, index must have each class of 1:4 or 1:8")
}
ny = length(y)
if(ny != length(index)){
stop("index must be provided for each mouse, length(y) != length(index)")
}
if(ny != length(kappas)){
stop("kappas must be provided for each mouse, length(y) != length(kappas)")
}
if(trecase){
nn = length(n)
nn0B = length(n0B)
if(nn != nn0B){
stop("allele specific counts mismatch: counts of allele B (n0B) don't match aggregate allele specific counts (n)")
}
f1.classes = unique(index[1:nn])
if(!all(f1.classes %in% f1)){
stop("data should be presented so that F1 mice are listed prior to inbred mice")
}
nya = sum(index %in% f1)
if(nya != nn){
stop("index doesn't correspond to the vector of allele specific reads (n), each element of n should have a corresponding class 1, 2, 5 or 6")
}
if(nclasses == 8 & length(coef) != 11){
stop("coef should be of length 11: add_F_trc, add_M_trc, add_F_ase, add_M_ase, poo_F, poo_M, beta_0, beta_kappa, beta_sex, beta_dom, beta_sex*dom")
}
if(nclasses == 4 & length(coef) != 6){
stop("coef should be of length 6: add_trc, add_ase, poo, beta_0, beta_kappa, beta_dom")
}
}else{
if(nclasses == 8 & length(coef) != 9){
stop("coef should be of length 9: add_F_trc, add_M_trc, beta_0, beta_kappa, beta_sex, beta_dom, beta_sex*dom, beta_poo_F, beta_poo_M")
}
if(nclasses == 4 & length(coef) != 5){
stop("coef should be of length 5: add_trc, beta_0, beta_kappa, beta_dom, beta_poo")
}
}
return(0)
}
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