/
realdata_rv144.R
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/
realdata_rv144.R
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res <-readRDS("res.rds") # only CD4+
meta <-readRDS("meta.rds")
cd4_counts <- readRDS("cd4_counts.rds")
#names(rv144)
#rv144$pheno.name
#exprs(rv144$continuous.data[[1]])
#exprs(rv144$continuous.data[[1]])[,c(14,7,12,9,5,16)]
#rv144.continuous<-lapply(rv144$continuous.data,function(x)x[,c(14,7,12,9,5,15)])
#rv144.continuous<-lapply(rv144.continuous,exprs)
#########################################################
#########################################################
sub_negctrl_800 = which(meta$Stim =="negctrl 1" & meta$VISITNO == 800) # unstim & VISITNO
sub_negctrl_100 = which(meta$Stim =="negctrl 1" & meta$VISITNO == 100) # unstim & VISITNO
sub_stim_800= which(meta$Stim=="92TH023-ENV" & meta$VISITNO == 800) # stim & VISITNO
sub_stim_100 = which(meta$Stim=="92TH023-ENV" & meta$VISITNO == 100) # stim & VISITNO
subsub_800 = intersect(meta$PTID[sub_negctrl_800],meta$PTID[sub_stim_800])
subsub_100 = intersect(meta$PTID[sub_negctrl_100],meta$PTID[sub_stim_100])
sub_s=NULL; sub_u=NULL;
for ( i in 1:length(subsub_800)) {
sub_s =c(sub_s,which(meta$PTID[sub_stim_800]==as.numeric(subsub_800[i])))
sub_u = c(sub_u, which(meta$PTID[sub_negctrl_800]==as.numeric(subsub_800[i])))
}
sub_s = sub_stim_800[sub_s]; #index for the stim and unstim sample
sub_u = sub_negctrl_800[sub_u];
subs = NULL; subu= NULL;
for ( i in 1:length(subsub_100)) {
subs =c(subs,which(meta$PTID[sub_stim_100]==as.numeric(subsub_100[i])))
subu = c(subu, which(meta$PTID[sub_negctrl_100]==as.numeric(subsub_100[i])))
}
subs = sub_stim_100[subs]; #index for the stim and unstim sample
subu = sub_negctrl_100[subu];
sub_s = c(sub_s,subs);
sub_u = c(sub_u,subu);
#cd4
N_s = (cd4_counts[sub_s])
N_u = (cd4_counts[sub_u])
ys= vector(mode="list", length=length(sub_s));
yu =vector(mode="list", length=length(sub_u));
for (i in 1:length(sub_s)) {
ys[[i]] = res[[sub_s[i]]]
yu[[i]] = res[[sub_u[i]]]
}
placebo = meta$vaccine[sub_s]
###############################################################
library(caTools)
#library(R.basic)
I = length(yu);
M = dim(yu[[1]])[2]
K = 2^M;
K1=K-1;
y_u=yu; y_s = ys;
n_s = array(0,dim=c(I,K));
n_u = array(0,dim=c(I,K));
d = array(0,dim=c(K,M))
count=1;
for (kk in 1:M) {
set = combs(1:M,kk);
ll = dim(combs(1:M,kk));
for ( lll in 1:ll[1]) {
d[(count-1+lll),set[lll,]] = 1;
}
#count = count+nChooseK(M,kk);
count = count+choose(M,kk);
}
d = cbind(d,rowSums(d)); # last column the number of 1's
for (i in 1:I) {
count_s = 1; count_u = 1;
yui = 1*(yu[[i]]!=0)
ysi = 1*(ys[[i]]!=0)
for ( kk in 1:K1) {
if( length(yui)>0) {
sel = apply(yui,1,function(xrow)(identical(as.numeric(xrow),as.numeric(d[kk,1:M]))))
n_u[i,kk] = sum(sel)
if(n_u[i,kk]>0) {
y_u[[i]][count_u:(count_u+n_u[i,kk]-1),] = yu[[i]][sel,]
count_u = count_u+n_u[i,kk]
}
}
if(length(ysi)>0) {
sel = apply(ysi,1,function(xrow)(identical(as.numeric(xrow),as.numeric(d[kk,1:M]))))
n_s[i,kk] = sum(sel)
if(n_s[i,kk]>0) {
y_s[[i]][count_s:(count_s+n_s[i,kk]-1),] = ys[[i]][sel,]
count_s = count_s+n_s[i,kk]
}
}
}
n_s[i,K] = N_s[i]-sum(n_s[i,1:K1])
n_u[i,K] = N_u[i]-sum(n_u[i,1:K1])
}
#######take off zero columns #############
nu0 = which(colSums(n_u)==0)
ns0 = which(colSums(n_s)==0)
n0 = intersect(nu0,ns0)
d = d[-n0,]
n_s = n_s[,-n0]
n_u = n_u[,-n0]
K = K-length(n0)
#### additional delete #####
#del = c(7,17,21,22,23,24,26,29,34,35,37,38,39,40,42,43,46,47);
del = which(colSums(n_s)<=11);
for ( i in 1:I) {
cs = cumsum(n_s[i,]); cu = cumsum(n_u[i,]); posis = NULL; posiu = NULL;
for (j in del) {
if(n_s[i,j]>1) {
posis = c(posis, (cs[j-1]+1):cs[j])
} else if (n_s[i,j]==1) {
posis = c(posis,cs[j])
}
if(n_u[i,j]>1) {
posiu = c(posiu, (cu[j-1]+1):cu[j])
} else if (n_u[i,j] ==1) {
posiu = c(posiu,cu[j])
}
}
if (length(posis) >0) {y_s[[i]] = y_s[[i]][-posis,]}
if (length(posiu) >0) {y_u[[i]] = y_u[[i]][-posiu,]}
}
d = d[-del,]
n_s = n_s[,-del]
n_u = n_u[,-del]
K = dim(n_s)[2]
K1=K-1;
n_s=matrix(as.integer(n_s),nrow=I)
n_u=matrix(as.integer(n_u),nrow=I)
d=matrix(as.integer(d),nrow=K)