Nothing
`proc.trec.X` =
function(rc, hessian=FALSE){
index = rc$index
y = rc$y
kappas = rc$kappas
tausB = rc$tausB
genes.switch = rc$genes.switch
geneids = rc$geneids
if(is.null(geneids)){geneids = 1:nrow(y)}
if(nrow(y) != length(geneids)){
stop("geneids length is not equal to the number of rows of y")
}
if(ncol(y) != length(index)){
stop("number of columns of y should match length of index")
}
na = sum(index %in% 1:2)
#genes.switch="ENSMUSG00000086503"
twosex = max(index)>4
if(twosex){
if(!all((1:8) %in% index)){
stop("package expects to have both sexes of all 4 groups: AB, BA, AA, BB")
}
ind.lst = lapply(1:8, function(i){which(index %in% i)})
}else{
if(!all((1:4) %in% index)){
stop("package expects to have all 4 groups: AB, BA, AA, BB")
}
ind.lst = lapply(1:4, function(i){which(index %in% i)})
}
if(is.null(kappas)){
kappas = colSums(y)
}else{
if(ncol(y) != length(kappas)){
stop("number of columns of y should match length of kappas")
}
}
if(is.null(tausB)){
F1.f = which(index %in% c(1, 2))
tausB = rep(.5,length(F1.f))
l.tau.b = l.tau.a = rep(log(.5), length(F1.f))
l.tau.r = rep(0, length(F1.f))
warning("Xce effect was not provided, program assumes there is no Xce effect.")
}else{
if(na != length(tausB)){
stop("number of columns of n should match length of tausB")
}
l.tau.a = log(1 - tausB); l.tau.b = log(tausB)
l.tau.r = log(tausB) - l.tau.a
}
l.tau.a = matrix(c(l.tau.a, l.tau.b), ncol=2)
l.tau.r = matrix(c(l.tau.r, -l.tau.r), ncol=2)
#maxtrial = 10;
eps.sh = 1E-3;maxiter.sh = 100
eps = 1E-3;maxiter = 100
iphi = 2;theta = .5
ngenes = length(geneids)
#genes.switch = c("ENSMUSG00000087640", "ENSMUSG00000086503", "ENSMUSG00000079481", "ENSMUSG00000079444")
ind = rep(1, ngenes)
if(length(genes.switch)>0){
switch.ind = unique(unlist(sapply(genes.switch, grep, geneids)))
ind[switch.ind] = 2
message("found ", length(switch.ind), " genes to switch Xce effect:")
for(i in switch.ind){
message(geneids[i])
}
}
nsamples = length(index)
intercept = poo = dev = dom = rep(0, length(index))
intercept = intercept + 1
dom[index %in% c(1, 2)] = 1
dev[index %in% c(5, 6)] = 1
poo[index == 1] = 1
poo[index == 2] = -1
if(twosex){
sex.tot = intercept;sex.tot[index>4] = -1
X = cbind(intercept, kappas, sex.tot, dom, dev, poo)
X.sex = X[, -3]
X.dom = X[, -4]
X.dev = X[, -5]
X.poo = X[, -6]
full.model = 2 + ncol(X)
#add.df = 3; poo.df = 1; dom.df = 1; add.trc.ase = 1; ase.add = 1; sex.df = 2; sex.add.df = 1; dev.df = 1
df=c(2, 1, 1, 2, 1, 1)
pvals = matrix(NA, nrow=ngenes, ncol=length(df))
colnames(pvals) = c("pval_add", "pval_poo", "pval_dom", "pval_sex", "pval_sex.add", "pval_dev")
coef.full = matrix(NA, nrow=ngenes, ncol=full.model + 2)
colnames(coef.full) = c("add_F_trc", "add_M_trc", "interc", "kappa", "sex", "dom", "dev.dom", "poo", "ll", "phi")
}else{
X = cbind(intercept, kappas, dom, poo)
X.dom = X[, -3]
X.poo = X[, -4]
full.model = 1 + ncol(X)
#add.df = 3; poo.df = 1; dom.df = 1; add.trc.ase = 1
df=c(1, 1, 1)
pvals = matrix(NA, nrow=ngenes, ncol=length(df))
colnames(pvals) = c("pval_add", "pval_poo", "pval_dom")
coef.full = matrix(NA, nrow=ngenes, ncol=full.model + 2)
colnames(coef.full) = c("add_trc", "interc", "kappa", "dom", "poo", "ll", "phi")
}
ll.ind = full.model + 1;phi.ind = ll.ind + 1
rownames(pvals) = geneids
rownames(coef.full) = geneids
coef.add = coef.poo = coef.dom = coef.full
coef.sex = coef.sex.add = coef.dev.dom = coef.add
message("processing ", ngenes, " genes")
errorlist = NULL
j = 1
if(twosex){
for(j in 1:ngenes){
if(j%%100 == 0){
message(j, "th gene")
}
#fit the smallest first
#6. sex effect: b0F' - b0M'=b0F - b0M=b1F - b1M=beta2=beta4=0
inits.sex = c(0, -5, 1, 0, 0, 0)
res.sex = trec.sex.X(yi=y[j, ], ind.lst=ind.lst, X=X.sex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.sex, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
if(is.null(res.sex)){
inits.poo = c(0, 0, -5, 1, 0, 0, 0)
inits.add = c(-5, 1, 0, 0, 0, 0)
inits.dom = c(0, 0, -5, 1, 0, 0, 0)
inits.dev = c(0, 0, -5, 1, 0, 0, 0)
inits.sex.add = c(0, -5, 1, 0, 0, 0)
}else{
inits.add = res.sex[3:8]
inits.poo = res.sex[1:7]
inits.dom = res.sex[c(1:5, 7:8)]
inits.dev = res.sex[c(1:6, 8)]
inits.sex.add = res.sex[2:8]
}
#2. POE
res.poo = trec.b1.X(yi=y[j, ], ind.lst=ind.lst, X=X.poo, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.poo, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#1. Strain
res.add = trec.b0.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.add, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#3. Dominance
res.dom = trec.dom.X(yi=y[j, ], ind.lst=ind.lst, X=X.dom, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.dom, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#8. Deviating dominance
res.dev = trec.dev.X(yi=y[j, ], ind.lst=ind.lst, X=X.dev,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.dev, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#7. sex specific addain: b0F' - b0M'=b0F - b0M=0
res.sex.add = trec.sex.b0.X(yi=y[j, ], ind.lst=ind.lst, X=X,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.sex.add, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#find better start for full
#"pval_add", "pval_poo", "pval_dom", "pval_sex", "pval_sex.add", "pval_dev"
lls = list(res.add, res.poo, res.dom, res.sex, res.sex.add, res.dev)
if(all(sapply(lls, is.null))){
errorlist = c(errorlist, j)
warning("no test ", j)
next
}
new.inits = get.inits(lst=lls, ind=ll.ind, trecase=FALSE)
#fit full
res.full = trec.full.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=new.inits$inits, iphi=new.inits$iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
if(is.null(res.full)){
errorlist = c(errorlist, j)
warning("no test ", j)
next
}
iphi_i = res.full[phi.ind]
#refit add
inits.add = res.full[3:8]
inits.poo = res.full[1:7]
inits.dom = res.full[c(1:5, 7:8)]
inits.dev = res.full[c(1:6, 8)]
inits.sex = c(mean(res.full[1:2]), res.full[c(3:4, 6:8)])
inits.sex.add = c(mean(res.full[1:2]), res.add[3:8])
res.add1 = trec.b0.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.add, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#refit poo
res.poo1 = trec.b1.X(yi=y[j, ], ind.lst=ind.lst, X=X.poo, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.poo, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#refit dom
res.dom1 = trec.dom.X(yi=y[j, ], ind.lst=ind.lst, X=X.dom, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.dom, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#refit sex
res.sex1 = trec.sex.X(yi=y[j, ], ind.lst=ind.lst, X=X.sex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.sex, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#5. refit sex specific addain
res.sex.add1 = trec.sex.b0.X(yi=y[j, ], ind.lst=ind.lst, X=X,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.sex.add, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#7. sex specific Dominance
res.dev1 = trec.dev.X(yi=y[j, ], ind.lst=ind.lst, X=X.dev,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.dev, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
res.add = get.better(lst=list(res.add, res.add1), ind=ll.ind, trecase=FALSE)
res.poo = get.better(lst=list(res.poo, res.poo1), ind=ll.ind, trecase=FALSE)
res.dom = get.better(lst=list(res.dom, res.dom1), ind=ll.ind, trecase=FALSE)
res.sex = get.better(lst=list(res.sex, res.sex1), ind=ll.ind, trecase=FALSE)
res.sex.add = get.better(lst=list(res.sex.add, res.sex.add1), ind=ll.ind, trecase=FALSE)
res.dev = get.better(lst=list(res.dev, res.dev1), ind=ll.ind, trecase=FALSE)
#find better start for full
#c("pval_add", "pval_poo", "pval_dom", "pval_sex", "pval_sex.add", "pval_dev")
lls = list(res.full, res.add, res.poo, res.dom, res.sex, res.sex.add, res.dev)
if(all(sapply(lls, is.null))){
errorlist = c(errorlist, j)
warning("no test ", j)
next
}
new.inits = get.inits(lst=lls, ind=ll.ind, trecase=FALSE)
#fit full
res.full1 = trec.full.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=new.inits$inits, iphi=new.inits$iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
res.full = get.better(lst=list(res.full, res.full1), ind=ll.ind, trecase=FALSE)
coef.full[j, ] = res.full
tests = test(full=res.full, short=lls[-1], df=df, ind=ll.ind, twosex=twosex, genei=j)
pvals[j, ] = tests$pvals
errorlist = c(errorlist, tests$error)
if(!is.null(res.add)){coef.add[j, ] = res.add}
if(!is.null(res.poo)){coef.poo[j, ] = res.poo}
if(!is.null(res.dom)){coef.dom[j, ] = res.dom}
if(!is.null(res.sex)){coef.sex[j, ] = res.sex}
if(!is.null(res.sex.add)){coef.sex.add[j, ] = res.sex.add}
if(!is.null(res.dev)){coef.dev.dom[j, ] = res.dev}
}
coef.full[, phi.ind] = 1/coef.full[, phi.ind]
coef.add[, phi.ind] = 1/coef.add[, phi.ind]
coef.poo[, phi.ind] = 1/coef.poo[, phi.ind]
coef.dom[, phi.ind] = 1/coef.dom[, phi.ind]
coef.sex[, phi.ind] = 1/coef.sex[, phi.ind]
coef.sex.add[, phi.ind] = 1/coef.sex.add[, phi.ind]
coef.dev.dom[, phi.ind] = 1/coef.dev.dom[, phi.ind]
#c("pval_add", "pval_poo", "pval_dom", "pval_sex", "pval_sex.add", "pval_dev.dom")
res = list(pvals=pvals, coef.full=coef.full, coef.add=coef.add, coef.poo=coef.poo,
coef.dom=coef.dom, coef.sex=coef.sex, coef.sex.add=coef.sex.add, coef.dev.dom=coef.dev.dom,
errorlist=errorlist)
}else{
for(j in 1:ngenes){
#for(j in 1:2){
if(j%%100 == 0){
message(j, "th gene")
}
#fit the smallest first
#1. Strain
inits.add = c(-5, 1, 0, 0)
#yi=y[j, ];sex=sex.ase; ni=nis[j, ];ni0=ni0B[j, ];start=inits.add
res.add = trec.b0.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.add, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
if(is.null(res.add)){
inits.poo = c(0, -5, 1, 0)
inits.dom = c(0, -5, 1, 0)
}else{
inits.poo = res.add[1:4]
inits.dom = res.add[c(1:3, 5)]
}
#2. POE
res.poo = trec.b1.X(yi=y[j, ], ind.lst=ind.lst, X=X.poo, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.poo, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#3. Dominance
res.dom = trec.dom.X(yi=y[j, ], ind.lst=ind.lst, X=X.dom, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.dom, iphi=iphi, maxiter=maxiter.sh, eps=eps.sh, tech.ctrl=rc$tech.ctrl)
#find better start for full
lls = list(res.add, res.poo, res.dom)
if(all(sapply(lls, is.null))){
errorlist = c(errorlist, j)
warning("no test ", j)
next
}
new.inits = get.inits(lst=lls, ind=ll.ind, trecase=FALSE)
#fit full
res.full = trec.full.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=new.inits$inits, iphi=new.inits$iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
if(is.null(res.full)){
errorlist = c(errorlist, j)
warning("no test ", j)
next
}
iphi_i = res.full[phi.ind]
#refit add
inits.add = res.full[2:5]
inits.poo = res.full[c(1:2, 4:5)]
inits.dom = res.full[1:4]
res.add1 = trec.b0.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.add, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#refit poo
res.poo1 = trec.b1.X(yi=y[j, ], ind.lst=ind.lst, X=X.poo, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.poo, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
#refit dom
res.dom1 = trec.dom.X(yi=y[j, ], ind.lst=ind.lst, X=X.dom, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=inits.dom, iphi=iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
res.add = get.better(lst=list(res.add, res.add1), ind=ll.ind, trecase=FALSE)
res.poo = get.better(lst=list(res.poo, res.poo1), ind=ll.ind, trecase=FALSE)
res.dom = get.better(lst=list(res.dom, res.dom1), ind=ll.ind, trecase=FALSE)
#find better start for full
lls = list(res.full, res.add, res.poo, res.dom)
if(all(sapply(lls, is.null))){
errorlist = c(errorlist, j)
warning("no test ", j)
next
}
new.inits = get.inits(lst=lls, ind=ll.ind, trecase=FALSE)
#fit full
res.full1 = trec.full.X(yi=y[j, ], ind.lst=ind.lst, X=X, twosex=twosex,
l.tau.r=l.tau.r[, ind[j]], l.tau.a=l.tau.a[, ind[j]],
start=new.inits$inits, iphi=new.inits$iphi_i, maxiter=maxiter, eps=eps, tech.ctrl=rc$tech.ctrl)
res.full = get.better(lst=list(res.full, res.full1), ind=ll.ind, trecase=FALSE)
coef.full[j, ] = res.full
tests = test(full=res.full, short=lls[-1], df=df, ind=ll.ind, twosex=twosex, genei=j)
pvals[j, ] = tests$pvals
errorlist = c(errorlist, tests$error)
if(!is.null(res.add)){coef.add[j, ] = res.add}
if(!is.null(res.poo)){coef.poo[j, ] = res.poo}
if(!is.null(res.dom)){coef.dom[j, ] = res.dom}
}
coef.full[, phi.ind] = 1/coef.full[, phi.ind]
coef.add[, phi.ind] = 1/coef.add[, phi.ind]
coef.poo[, phi.ind] = 1/coef.poo[, phi.ind]
coef.dom[, phi.ind] = 1/coef.dom[, phi.ind]
res = list(pvals=pvals, coef.full=coef.full, coef.add=coef.add, coef.poo=coef.poo,
coef.dom=coef.dom, errorlist=errorlist)
}
if(hessian){
if(ngenes>100)warning("This option is recommended only for the extra analysis on a subset of genes.")
hess.lst = as.list(rep(NA, ngenes))
for(j in 1:ngenes){
tag = tryCatch({
nll = nLogLik.trec.X(coef=coef.full[j, 1:(ll.ind-1)], phi=coef.full[j, phi.ind],
rc, j, hessian=TRUE)
hess.lst[[j]] = nll$hess
0
}, error=function(e) {
warning("a problem with hessian")
1
})
names(hess.lst) = geneids
}
res$hess.lst = hess.lst
}
return(res)
}
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