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RMA
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@elijahedmondson
elijahedmondson committed Sep 7, 2016
1 parent 19839d4 commit 8955250
Showing 1 changed file with 44 additions and 28 deletions.
72 changes: 44 additions & 28 deletions 8. Resample model averaging.R
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Expand Up @@ -68,7 +68,7 @@ bootstrap <- HS.assoc.bootstrap(perms = 200, chr = 4, pheno = Gamma, pheno.col =



Cat2.AI.18 <- HS.cox.RMA.chrom(perms = 200, chr = 18, pheno = All.irr, pheno.col = "Cat2", days.col = "days2",
Cat.Allirr.13 <- HS.cox.RMA.chrom(perms = 200, chr = 13, pheno = All.irr, pheno.col = "Cat2", days.col = "days2",
probs, K, addcovar, markers, snp.file, outdir = "~/Desktop/",
tx = "All Irradiated", sanger.dir = "~/Desktop/R/QTL/WD/HS.sanger.files/")

Expand All @@ -84,7 +84,7 @@ MammaACA.Un <- HS.RMA.chrom(perms = 200, chr = 11, pheno = Un, pheno.col = "Mamm
tx = "Unirradiated", sanger.dir = "~/Desktop/R/QTL/WD/HS.sanger.files/")
MammaACA.AI <- HS.RMA.chrom(perms = 200, chr = 11, pheno = All.irr, pheno.col = "MammACA", probs, K, addcovar,
markers, snp.file, outdir = "~/Desktop/",
tx = "Unirradiated", sanger.dir = "~/Desktop/R/QTL/WD/HS.sanger.files/")
tx = "All Irradiated", sanger.dir = "~/Desktop/R/QTL/WD/HS.sanger.files/")

### PLOTTING BOOTSTRAP RESULTS (HISTOGRAM) ###
### PLOTTING BOOTSTRAP RESULTS (HISTOGRAM) ###
Expand All @@ -108,22 +108,22 @@ allirr = Thy.boot[which(Thy.boot$TX == "All.irradiated" & Thy.boot$AML.LOD > 5),

#HISTOGRAM
layout(matrix(3:1, 3, 1))
hist(un$average, breaks=150, col="blue", main = "Unirradiated", xlab="Chromosome 2", prob = T, xlim = c(0, 182113224))
hist(un$average, breaks=150, col="blue", main = "Unirradiated", xlab="Chromosome 1", prob = T, xlim = c(0, 125000000))
lines(density(un$average), col="black")
hist(gamma$average, breaks=150, col="green", main = "Gamma", xlab="Chromosome 2", prob = T, xlim = c(0, 182113224))
hist(gamma$average, breaks=150, col="green", main = "Gamma", xlab="Chromosome 1", prob = T, xlim = c(0, 125000000))
lines(density(gamma$average), col="black")
hist(hze$average, breaks=150, col="red", main = "HZE", xlab="Chromosome 2", prob = T, xlim = c(0, 182113224))
hist(hze$average, breaks=150, col="red", main = "HZE", xlab="Chromosome 1", prob = T, xlim = c(0, 125000000))
lines(density(hze$average), col="black", lwd = 1)

layout(matrix(4:1, 4, 1))
hist(un$AML.Locus, breaks=150, col="blue", main = "Unirradiated", xlab="Chromosome 2", prob = T, xlim = c(0, 182113224))
lines(density(un$AML.Locus), col="black")
hist(gamma$AML.Locus, breaks=150, col="green", main = "Gamma", xlab="", prob = T, xlim = c(0, 182113224))
lines(density(gamma$AML.Locus), col="black")
hist(hze$AML.Locus, breaks=150, col="red", main = "HZE", xlab="", prob = T, xlim = c(0, 182113224))
lines(density(hze$AML.Locus), col="black", lwd = 1)
hist(allirr$AML.Locus, breaks=150, col="black", main = "All Irradiated", xlab="", prob = T, xlim = c(0, 182113224))
lines(density(All.irradiated$AML.Locus), col="black", lwd = 1)
hist(un$average, breaks=150, col="blue", main = "Unirradiated", xlab="Chromosome 2", prob = T, xlim = c(0, 182113224))
lines(density(un$average), col="black")
hist(gamma$average, breaks=150, col="green", main = "Gamma", xlab="", prob = T, xlim = c(0, 182113224))
lines(density(gamma$average), col="black")
hist(hze$average, breaks=150, col="red", main = "HZE", xlab="", prob = T, xlim = c(0, 182113224))
lines(density(hze$average), col="black", lwd = 1)
hist(allirr$average, breaks=150, col="black", main = "All Irradiated", xlab="", prob = T, xlim = c(0, 182113224))
lines(density(All.irradiated$average), col="black", lwd = 1)

#HISTOGRAM WITHOUT DENSITY
layout(matrix(3:1, 3, 1))
Expand Down Expand Up @@ -171,41 +171,57 @@ title(main = "Nonparametric Bootstrap Resampling with Replacement: Distribution



boot <- read.csv("~/Desktop/Whole Chr Resample/Raw Data-MammACA 11.csv")

boot <- read.csv("~/Desktop/Whole Chr Resample/Raw Data-Cataract Chr 17.csv")
gamma = boot[which(boot$X == "gamma"),]
hze = boot[which(boot$X == "HZE"),]
un = boot[which(boot$X == "unirradiated"),]


merge.boot <- factor(boot$X, levels = c("gamma", "HZE", "unirradiated"),
labels = c("Gamma", "HZE", "Unirradiated"))
par(mfrow=c(1,1))
sm.density.compare(boot$average, boot$X, xlab = "Chromosome 17", lwd = 2.5)
title(main = "Resample Model Averaging: Cataract Chromosome 17")
sm.density.compare(boot$average, boot$X, xlab = "Chromosome 11", lwd = 2.5)
title(main = "Resample Model Averaging: Mammary Adenocarcinoma")
colfill = c(2:(2+length(levels(merge.boot))))
legend("topleft", levels(merge.boot), fill = colfill)

layout(matrix(3:1, 3, 1))
hist(un$average, breaks=150, col="blue", main = "Unirradiated", xlab="Chromosome 11", prob = T, xlim = c(0, 125000000))
lines(density(un$average), col="black")
hist(gamma$average, breaks=150, col="green", main = "Gamma", xlab="", prob = T, xlim = c(0, 125000000))
lines(density(gamma$average), col="black")
hist(hze$average, breaks=150, col="red", main = "HZE", xlab="", prob = T, xlim = c(0, 125000000))
lines(density(hze$average), col="black", lwd = 1)




boot <- read.csv("~/Desktop/Whole Chr Resample/Raw Data-Cataract Chr 13.csv")
gamma = boot[which(boot$X == "gamma"),]
hze = boot[which(boot$X == "HZE"),]
un = boot[which(boot$X == "unirradiated"),]
allirr = boot[which(boot$X == "allirr"),]


merge.boot <- factor(boot$X, levels = c("All.irradiated", "gamma", "HZE", "Unirradiated"),
merge.boot <- factor(boot$X, levels = c("allirr", "gamma", "HZE", "Unirradiated"),
labels = c("All Irradiated", "Gamma", "HZE", "Unirradiated"))
par(mfrow=c(1,1))
sm.density.compare(boot$average, boot$X, xlab = "Chromosome ", lwd = 2.5)
title(main = "AML Adenoma: Resample Model Averaging")
sm.density.compare(boot$average, boot$X, xlab = "Chromosome 13", lwd = 2.5)
title(main = "Resample Model Averaging: Cataractogenesis")
colfill = c(2:(2+length(levels(merge.boot))))
legend("topleft", levels(merge.boot), fill = colfill)


AML.boot <- factor(Thy.boot2$X, levels = c("All.irradiated", "gamma", "HZE", "Unirradiated"),
labels = c("All Irradiated", "Gamma", "HZE", "Unirradiated"))
par(mfrow=c(1,1))
sm.density.compare(boot$average, boot$X, xlab = "Chromosome 2", lwd = 2.5)
title(main = "Resample Model Averaging")
colfill = c(2:(2+length(levels(boot))))
legend("topright", levels(boot), fill = colfill)
#sm.binomial.bootstrap()

layout(matrix(4:1, 4, 1))
hist(un$average, breaks=150, col="blue", main = "Unirradiated", xlab="Chromosome 13", prob = T, xlim = c(0, 125000000))
lines(density(un$average), col="black")
hist(gamma$average, breaks=150, col="green", main = "Gamma", xlab="", prob = T, xlim = c(0, 125000000))
lines(density(gamma$average), col="black")
hist(hze$average, breaks=150, col="red", main = "HZE", xlab="", prob = T, xlim = c(0, 125000000))
lines(density(hze$average), col="black", lwd = 1)
hist(allirr$average, breaks=150, col="black", main = "All Irradiated", xlim = c(0, 125000000))
lines(density(allirr$average), col="black", lwd = 1)



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