Iterative Comparison - Male
Last updated: 2023-03-05
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Knit directory: dgrp-starve/
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#loop count and data limit
iter <- 48
#Parallel core count
#registerDoParallel(cores = 8)
#ggplot holder list
gg <- vector(mode='list', length=12)
# result storage elements
fit_greml <- vector(mode='list', length=iter)
fit_gbayesC <- vector(mode='list', length=iter)
fit_varbvs <- vector(mode='list', length=iter)
fit_glmnet <- vector(mode='list', length=iter)dataFlag <- TRUE
if(dataFlag){
#wolb infection and inversion status data with phenotype adjustment function
load("/data2/morgante_lab/data/dgrp/misc/adjustData.RData")
#expression data matched to line and starvation phenotype
#xp_f <- fread("data/xp-f.txt")
xp_m <- fread("data/xp-m.txt")
#setwd("C:/Users/noahk/OneDrive/Desktop/amogus")
#getwd()
#create matrix of only gene expression, trims line and starvation
X <- as.matrix(xp_m[,3:13577])
rownames(X) <- xp_m[,line]
W <- scale(X)
y_temp <- xp_m[,starvation]
dat <- data.frame(id=xp_m[,line], y=y_temp)
y <- adjustPheno(dat, "starvation")
} else{
# Toy Data set, 200x100 matrix
W <- matrix(rnorm(20000), ncol = 100)
colnames(W) <- paste0("gene", 1:ncol(W))
rownames(W) <- paste0("line", 1:nrow(W))
#model uses genes 1:5 and 10:20
y <- rowSums(W[, 1:5]) + rowSums(W[, 10:20]) + rnorm(nrow(W))
}Type III ANOVA table for covariates: starvation
Df Sum of Sq RSS AIC F value Pr(>F)
<none> 15975 893.32
factor(wolba) 1 3.041 15978 891.35 0.0354 0.8509
factor(In_2L_t) 2 299.141 16274 892.99 1.7415 0.1781
factor(In_2R_NS) 2 243.044 16218 892.31 1.4149 0.2455
factor(In_3R_P) 2 230.105 16205 892.15 1.3396 0.2645
factor(In_3R_K) 2 288.050 16263 892.85 1.6770 0.1898
factor(In_3R_Mo) 2 207.445 16182 891.87 1.2077 0.3012
Estimated effects
Estimate Std. Error t value Pr(>|t|)
(Intercept) 45.6614374 1.157976 39.4321227 2.909220e-92
factor(wolba)y -0.2574606 1.368248 -0.1881681 8.509500e-01
factor(In_2L_t)1 1.7198329 2.311372 0.7440744 4.577704e-01
factor(In_2L_t)2 -3.7780449 2.348592 -1.6086422 1.093906e-01
factor(In_2R_NS)1 -1.0811449 3.443957 -0.3139252 7.539297e-01
factor(In_2R_NS)2 5.8594026 3.595753 1.6295343 1.048923e-01
factor(In_3R_P)1 -2.0731924 3.879580 -0.5343858 5.937128e-01
factor(In_3R_P)2 7.1994131 4.718118 1.5259077 1.287315e-01
factor(In_3R_K)1 5.3513957 3.043456 1.7583284 8.033635e-02
factor(In_3R_K)2 3.7673764 6.668091 0.5649857 5.727643e-01
factor(In_3R_Mo)1 -3.0569154 3.189101 -0.9585510 3.390293e-01
factor(In_3R_Mo)2 -3.0977753 2.402719 -1.2892793 1.989020e-01### qgg_greml
#model to solve for, vector of ones
mu <- matrix(rep(1, length(y)), ncol=1)
#names(mu) <- paste0("line", 1:length(mu))
rownames(mu) <- xp_m[,line]
TRM <- tcrossprod(W)/ncol(W)
# k-fold parameters
n <- length(y)
fold <- 10
iter <- 48### sample analysis of gbayesC to show that convergence is working as expected
test_IDs <- sample(1:n, as.integer(n / fold))
W_train <- W[-test_IDs,]
W_test <- W[test_IDs,]
y_train <- y[-test_IDs]
y_test <- y[test_IDs]
### GBAYES-C
fitC <- qgg::gbayes(y=y_train, W=W_train, method="bayesC", scaleY=FALSE, nit=10000, nburn=5000)plotCustomBayes <- function(rdsPath){
# data read in is a gBayes fit object from qgg
#fitC <- readRDS("gbayesC-f.Rds")
fitC <- readRDS(rdsPath)
# calculate column narrow heritability
fitC$h2 <- fitC$vgs/(fitC$vgs+fitC$ves)
# data is extracted and stored
fitData <- data.table(iter=1:10000, ves=fitC$ves, vbs=fitC$vbs, vgs=fitC$vgs, h2=fitC$h2)
gg <- vector(mode='list', length=4)
gg[[1]] <- ggplot(fitData, aes(x=iter, y=ves)) +
geom_point(size=0.5) +
labs(x="Iteration", y="Ve") +
ggtitle("Posterior Mean for Residual Variance")
gg[[2]] <- ggplot(fitData, aes(x=iter, y=vbs)) +
geom_point(size=0.5) +
labs(x="Iteration", y="Vb") +
ggtitle("Posterior Mean for Marker Variance")
gg[[3]] <- ggplot(fitData, aes(x=iter, y=vgs)) +
geom_point(size=0.5) +
labs(x="Iteration", y="Vg") +
ggtitle("Posterior Mean for Genomic Variance")
gg[[4]] <- ggplot(fitData, aes(x=iter, y=ves)) +
geom_point(size=0.5) +
labs(x="Iteration", y="h^2") +
ggtitle("Posterior Mean for Narrow-sense Heritability")
return(gg)
}
# fit taken from one iteration, restored from Rds using code chunk shown above
#fitC <- readRDS("data/gbayesC-m.Rds")
plotHold <- plotCustomBayes("data/gbayesC-m.Rds")
plot_grid(plotHold[[1]],plotHold[[2]], ncol=2)
plot_grid(plotHold[[3]],plotHold[[4]], ncol=2)
#plotBayes(fit=fitC, what="trace")#this runs on the same data sets as greml
### qgg_gBayesC
### https://www.rdocumentation.org/packages/qgg/versions/1.1.1/topics/gbayes
# Bayes C: uses a “rounded spike” (low-variance Gaussian) at origin many small effects can contribute to polygenic component, reduces the dimensionality of the model (makes Gibbs sampling feasible).
#Parallel Header
#tempResult <-
iter <- 1
corLoop <- foreach(i=1:iter) %dopar% {
#Linear Header
#for(i in 1:iter){
corResult <- (1:4)
#setup train and test sets with trait vectors
test_IDs <- sample(1:n, as.integer(n / fold))
W_train <- W[-test_IDs,]
W_test <- W[test_IDs,]
y_train <- y[-test_IDs]
y_test <- y[test_IDs]
### GREML, qgg package
fitGreml <- qgg::greml(y=y, X=mu, GRM=list(A=TRM), validate = matrix(test_IDs,ncol=1), verbose=FALSE)
#Store coeff directly
fit_greml[[i]] <- fitGreml$accuracy$Corr
corResult[1] <- fitGreml$accuracy$Corr
### GBAYES-C
fitC <- qgg::gbayes(y=y_train, W=W_train, method="bayesC", scaleY=FALSE, nit=10000, nburn=5000)
# expected/calculated value for y_test
# \hat{y}_test = W_{test} * \hat{b} + \hat{mu}
y_calc <- W_test %*% fitC$b + mean(y_train)
# store coeff
fit_gbayesC[[i]] <- cor(y_test, y_calc)
corResult[2] <- cor(y_test, y_calc)
if(i==1){
print(paste0("gbayesC trace plots from validate set ",i))
plotBayes(fit=list(fitC), what = "trace")
}
### VARBVS
fitVarb <- varbvs::varbvs(X = W_train, NULL, y=y_train, family = "gaussian", logodds=seq(-3.5,-1,0.1), sa = 1, verbose=FALSE)
# \hat{y}_test = W_{test} * \hat{b} + \hat{mu}
y_calc <- W_test %*% fitVarb$beta + mean(y_train)
fit_varbvs[[i]] <- cor(y_test, y_calc)
corResult[3] <- cor(y_test, y_calc)
### GLMNET
fitlm <- glmnet::cv.glmnet(x=W_train, y=y_train, alpha=1)
b_hat <- glmnet::coef.glmnet(fitlm, s="lambda.min")
y_int <- b_hat[1]
b_hat <- b_hat[2:length(b_hat)]
y_calc <- W_test %*% b_hat + y_int
fit_glmnet[[i]] <- cor(y_test, y_calc)
corResult[4] <- cor(y_test, y_calc)
corResult
}# results loaded from correlation loop structure
corLoop <- readRDS("data/corLoop-m.rds")
for(i in 1:iter){
fit_greml[[i]] <- corLoop[[i]][1]
fit_gbayesC[[i]] <- corLoop[[i]][2]
fit_varbvs[[i]] <- corLoop[[i]][3]
fit_glmnet[[i]] <- corLoop[[i]][4]
}iter <- 48
bint <- 10
### qgg_greml
qgg_greml_data <- as.data.table(fit_greml)
qgg_greml_data <- transpose(qgg_greml_data)
colnames(qgg_greml_data) <- "cor"
#print(paste0("GREML"))
#print(paste0("Mean correlation coefficient: ", mean(qgg_greml_data[,cor])))
#print(paste0("Variance of correlation coefficient: ", var(qgg_greml_data)))
gg[[1]] <- ggplot(qgg_greml_data, aes(x=cor)) +
geom_histogram(bins=bint, fill='red') +
labs(x="Corr Coeff") +
ggtitle("GREML CV Correlations Histogram")
### qgg_gbayesC
qgg_gbayesC_data <- as.data.table(fit_gbayesC)
qgg_gbayesC_data <- transpose(qgg_gbayesC_data)
colnames(qgg_gbayesC_data) <- "cor"
#print(paste0("gBayesC"))
#print(paste0("Mean correlation coefficient: ", mean(qgg_gbayesC_data[,cor])))
#print(paste0("Variance of correlation coefficient: ", var(qgg_gbayesC_data)))
gg[[2]] <- ggplot(qgg_gbayesC_data, aes(x=cor)) +
geom_histogram(bins=bint, fill='red') +
labs(x="Corr Coeff") +
ggtitle("gBayesC Prediction Corr Histogram")
### VARBVS
varbvs_data <- as.data.table(fit_varbvs)
varbvs_data <- transpose(varbvs_data)
colnames(varbvs_data) <- "cor"
#print(paste0("VARBVS"))
#print(paste0("Mean correlation coefficient: ", mean(varbvs_data[,cor])))
#print(paste0("Variance of correlation coefficient: ", var(varbvs_data)))
gg[[3]] <- ggplot(varbvs_data, aes(x=cor)) +
geom_histogram(bins=bint, fill='red') +
labs(x="Corr Coeff") +
ggtitle("varbvs Prediction Corr Histogram")
### GLMNET
glmnet_data <- as.data.table(fit_glmnet)
glmnet_data <- transpose(glmnet_data)
colnames(glmnet_data) <- "cor"
#print(paste0("GLMNET"))
#print(paste0("Mean correlation coefficient: ", mean(glmnet_data[,cor])))
#print(paste0("Variance of correlation coefficient: ", var(glmnet_data)))
gg[[4]] <- ggplot(glmnet_data, aes(x=cor)) +
geom_histogram(bins=bint, fill='red') +
labs(x="Corr Coeff") +
ggtitle("glmnet Prediction Corr Histogram")result <- data.table(method="greml", meanCoeff=mean(qgg_greml_data[,cor]))
result[,varCoeff := var(qgg_greml_data)]
temp <- data.table(method="gBayesC", meanCoeff=mean(qgg_gbayesC_data[,cor]))
temp[,varCoeff := var(qgg_gbayesC_data)]
result <- rbind(result, temp)
temp <- data.table(method="varbvs", meanCoeff=mean(varbvs_data[,cor]))
temp[,varCoeff := var(varbvs_data)]
result <- rbind(result, temp)
temp <- data.table(method="glmnet", meanCoeff=mean(glmnet_data[,cor]))
temp[,varCoeff := var(glmnet_data)]
result <- rbind(result, temp)
# Map the time of day to different fill colors
#gg[[5]] <- ggplot(data=result, aes(x=method, y=meanCoeff, fill=method)) +
#geom_bar(stat="identity")
#boxplot(result$meanCoeff)
gg[[5]] <- ggplot(data=result, aes(x=method, y=meanCoeff, fill=method)) +
geom_bar(stat="identity") +
ggtitle("Mean Correlation Coefficient by Method")
gg[[6]] <- ggplot(data=result, aes(x=method, y=varCoeff, fill=method)) +
geom_bar(stat="identity") +
ggtitle("Variance of Coefficients by Method")
#gg[[5]] <- ggplot(result, aes(x=meanCoeff)) +
# geom_boxplot() +
# coord_flip()
#gg[[6]] <- ggplot(result, aes(x=varCoeff)) +
# geom_boxplot() +
# coord_flip()Correlation Coefficient Histograms
print("Correlation coefficient histograms")[1] "Correlation coefficient histograms"plot_grid(gg[[1]],gg[[2]],gg[[3]],gg[[4]], ncol=2)
Method Comparison Summary
plot_grid(gg[[5]],gg[[6]], ncol=2)
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.5 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /opt/ohpc/pub/Software/openblas_0.3.10/lib/libopenblas_haswellp-r0.3.10.dev.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] glmnet_4.1-6 Matrix_1.5-3 varbvs_2.5-16 qgg_1.1.1
[5] doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2 qqman_0.1.8
[9] cowplot_1.1.1 ggplot2_3.4.1 data.table_1.14.8 dplyr_1.1.0
[13] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 lattice_0.20-45 png_0.1-7
[4] getPass_0.2-2 ps_1.6.0 rprojroot_2.0.3
[7] digest_0.6.29 utf8_1.2.2 R6_2.5.1
[10] MatrixModels_0.5-1 evaluate_0.15 coda_0.19-4
[13] highr_0.9 httr_1.4.2 pillar_1.7.0
[16] rlang_1.0.6 rstudioapi_0.13 SparseM_1.81
[19] whisker_0.4 callr_3.7.0 jquerylib_0.1.4
[22] rmarkdown_2.17 labeling_0.4.2 splines_4.0.3
[25] statmod_1.5.0 stringr_1.4.0 munsell_0.5.0
[28] compiler_4.0.3 httpuv_1.6.5 xfun_0.30
[31] pkgconfig_2.0.3 shape_1.4.6 mcmc_0.9-7
[34] htmltools_0.5.2 tidyselect_1.2.0 tibble_3.1.6
[37] codetools_0.2-18 fansi_1.0.3 calibrate_1.7.7
[40] crayon_1.5.1 withr_2.5.0 later_1.3.0
[43] MASS_7.3-56 grid_4.0.3 jsonlite_1.8.0
[46] gtable_0.3.0 lifecycle_1.0.3 git2r_0.30.1
[49] magrittr_2.0.3 scales_1.2.0 cli_3.6.0
[52] stringi_1.7.6 farver_2.1.0 fs_1.5.2
[55] promises_1.2.0.1 latticeExtra_0.6-29 bslib_0.3.1
[58] ellipsis_0.3.2 generics_0.1.2 vctrs_0.5.2
[61] nor1mix_1.3-0 RColorBrewer_1.1-3 tools_4.0.3
[64] glue_1.6.2 jpeg_0.1-9 survival_3.3-1
[67] processx_3.5.3 fastmap_1.1.0 yaml_2.3.5
[70] colorspace_2.0-3 knitr_1.38 sass_0.4.1
[73] quantreg_5.94 MCMCpack_1.6-3