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July 19, 2017 09:23
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## sharing parameter, largish, so we expect to see a big enough difference to check if working | |
S <- 100 | |
prior.bin.fn <- function(nT1,s=100,mT1=3) { | |
dbinom(nT1,size=s,prob=mT1/s)/choose(s,nT1) | |
} | |
bothpp <- function(data) { | |
ss1 <- strsplit(data$t1.str,"%") | |
ss2 <- strsplit(data$t2.str,"%") | |
data$overlap <- sapply(1:nrow(data), function(i) | |
length(intersect(ss1[[i]],ss2[[i]]))>0) | |
data$apr <- prior.bin.fn(data$t1.size) * prior.bin.fn(data$t2.size) * ifelse(data$overlap,S,1) | |
data$apr <- data$apr/sum(data$apr) | |
data$pp <- MTFM:::calcpp(data$apr,data$t1t2.logbf) | |
data$rpr <- prior.bin.fn(data$t1.size) * prior.bin.fn(data$t2.size) | |
data$rpr <- data$rpr/sum(data$rpr) | |
data$rpp <- MTFM:::calcpp(data$rpr,data$t1t2.logbf) | |
return(data) | |
} | |
makeM <- function(str,usnps) { | |
M <- matrix(0,length(str),length(usnps),dimnames=list(NULL,usnps)) | |
ss <- strsplit(str,"%") | |
for(i in seq_along(ss)) | |
M[i,ss[[i]]] <- 1 | |
return(M) | |
} | |
library(MTFM) | |
library(data.table) | |
margpp <- function(data) { | |
dt <- as.data.table(data) | |
d1 <- (dt[,.(t1.logbf=unique(t1.logbf),t1.size=unique(t1.size),pp.orig=sum(pp),rpp.orig=sum(rpp)), | |
by=c("t1.str")]) | |
d2 <- (dt[,.(t2.logbf=unique(t2.logbf),t2.size=unique(t2.size),pp.orig=sum(pp),rpp.orig=sum(rpp)), | |
by=c("t2.str")]) | |
setnames(d1,c("str","logbf","size","spp.orig","mpp.orig")) | |
setnames(d2,c("str","logbf","size","spp.orig","mpp.orig")) | |
d1 <- unique(d1,by="str") | |
d2 <- unique(d2,by="str") | |
d1$pr <- prior.bin.fn(d1$size) | |
d2$pr <- prior.bin.fn(d2$size) | |
d1$mpp.direct <- MTFM:::calcpp(d1$pr,d1$logbf) | |
d2$mpp.direct <- MTFM:::calcpp(d2$pr,d2$logbf) | |
ss1 <- strsplit(data$t1.str,"%") | |
ss2 <- strsplit(data$t2.str,"%") | |
usnps <- unique(unlist(c(ss1,ss2))) | |
length(usnps) | |
M1 <- makeM(d1$str,usnps) | |
M2 <- makeM(d2$str,usnps) | |
PP <- marginalpp2(M1,M2,d1$logbf,d2$logbf,d1$pr,d2$pr,S,prior.bin.fn(0)) | |
d1$spp.new <- as.numeric(PP$shared.pp1)[-1] | |
d1$mpp.new <- as.numeric(PP$single.pp1)[-1] | |
d2$spp.new <- as.numeric(PP$shared.pp2)[-1] | |
d2$mpp.new <- as.numeric(PP$single.pp2)[-1] | |
return(list(d1=d1,d2=d2)) | |
} | |
## load data | |
data <- read.table("/scratch/wallace/IL2RA/AD-AC-rep_100-bf-final.txt",header=TRUE,as.is=TRUE) | |
## analyse | |
data <- bothpp(data) | |
marg <- margpp(data) | |
head(marg$d1[,.(str,mpp.orig,mpp.direct,mpp.new)]) | |
head(marg$d1[,.(str,spp.orig,spp.new)]) | |
## mpp (marginal, unshared) matches, but not aggregating over orig | |
## spp (marginal, shared) doesn't match | |
nrow(data) | |
nrow(marg$d1) * nrow(marg$d2) | |
## is it because data has only a subset of possible model pairs? | |
adata <- expand.grid(1:nrow(d1),1:nrow(d2)) | |
adata <- cbind(adata,marg$d1[adata$Var1,.(str,logbf,size)]) | |
adata <- cbind(adata,marg$d2[adata$Var2,.(str,logbf,size)]) | |
colnames(adata)[-c(1:2)] <- c("t1.str","t1.logbf","t1.size","t2.str","t2.logbf","t2.size") | |
adata$t1t2.logbf <- adata$t1.logbf + adata$t2.logbf - 46.6 | |
## now perform same analysis as above | |
adata <- bothpp(adata) | |
amarg <- margpp(adata) | |
head(amarg$d1[,.(str,mpp.orig,mpp.direct,mpp.new)]) | |
head(amarg$d1[,.(str,spp.orig,spp.new)]) | |
with(amarg$d1,plot(spp.orig,spp.new)) | |
## now mpp matches by all methods, but not spp | |
## write out marginalpp here in R | |
d1 <- amarg$d1 | |
d2 <- amarg$d2 | |
ss1 <- strsplit(d1$str,"%") | |
ss2 <- strsplit(d2$str,"%") | |
Qi <- numeric(nrow(d1)) | |
Oi <- numeric(nrow(d1)) | |
for(i in 1:nrow(d1)) { | |
Qi[i] <- 0 | |
for(j in 1:nrow(d2)) { | |
overlap <- length(intersect(ss1[[i]],ss2[[j]])) | |
if(overlap>0) | |
Qi[i] <- Qi[i] + d2$mpp.new[[j]] | |
else | |
Oi[i] <- Oi[i] + d2$mpp.new[[j]] | |
} | |
} | |
d1$alt2.pr <- d1$pr * (Oi + S * Qi) | |
d1$alt2.pr <- d1$alt2.pr / sum(d1$alt2.pr) | |
d1$spp.alt2 <- MTFM:::calcpp(d1$alt2.pr,d1$logbf) | |
d1$alt.pr <- d1$pr * (1 + (S-1) * Qi) | |
d1$alt.pr <- d1$alt.pr / sum(d1$alt.pr) | |
d1$spp.alt <- MTFM:::calcpp(d1$alt.pr,d1$logbf) | |
head(d1[,.(str,spp.orig,spp.new,spp.alt,spp.alt2)]) | |
## spp.alt matches spp.new, not spp.orig. | |
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