Simple Regression
Last updated: 2022-12-21
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Knit directory: dgrp-starve/
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Methodology
The lowest p-values were chosen to represent the fixed effect as better correlations assist in prediction of starvation resistance.
Random effect was a normal distribution with a mean of 1 and sd of 0.25
Depending on what is run, the system is not able to converge asa it either goes to positive infinity and overflows to a negative value or reaches zero and “converges” at zero. If this webpage renders, then both runs will have converged on zero.
Additionally, I left verbose on TRUE to observe iteration steps as while randomness is seeded, iteration steps were not the same every time.
Female
#read in p values
fReg <- fread("data/fRegress.txt")
#read in expression data
fMeans <- fread("data/fMeans.txt")
#create matrix of only gene expression, trims line and starvation
Y <- as.matrix(fMeans[,3:11340], row.names=1)
#dimensions and number of fixed effect genes
n <- dim(Y)[1]
p <- dim(Y)[2]
p_effect <- 525
#p_effect <- round(p / 15)
#400, 250 maxit
#keep
if(TRUE){
#error is seeded rnorm, number of rows(lines)
e <- rnorm(n, 1, 0.25)
# add gene names to p val list
geneNames <- colnames(fMeans)[3:11340]
fReg <- fReg[, gene:=geneNames]
###sorted p values
# LOW pval
pSort <- fReg[order(-pvalList)]
#HIGH pval
#pSort <- fReg[order(-pvalList)]
}
#rerun
if(TRUE){
# fixed effect vector USELESS, must be matched to certain values
b <- c(rnorm(p_effect, mean=6), rep(0, p-p_effect))
#affix vector to sorted p values
pSort[,b:=b]
#restore sort order to id/alphabetical gene, matches expression data order
fFin <- pSort[order(id)]
# PROPER fixed effect vector PROPER with proper indexing
b <- fFin[,b]
#matrix multiplication of the data and p
y <- drop(Y%*%b) + e
###Create model for covariates to adjust for (only an intercept in our case)
mu <- rep(1, length(y))
names(mu) <- names(y)
###Compute transcriptomic relationship matrix (accounts for structure based on expression levels)
W <- scale(Y)
TRM <- tcrossprod(W)/ncol(W)
}
###Fit mixed model
fit <- greml(y = y, X = mu, GRM = list(TRM), verbose = TRUE, maxit = 100)[1] "Iteration:" "1" "Theta:" "56.48" "55.88"
[1] "Iteration:" "2" "Theta:" "113.42" "109.86"
[1] "Iteration:" "3" "Theta:" "228.63" "212.22"
[1] "Iteration:" "4" "Theta:" "464.08" "395.55"
[1] "Iteration:" "5" "Theta:" "953.03" "683.97"
[1] "Iteration:" "6" "Theta:" "1986.92" "1000"
[1] "Iteration:" "7" "Theta:" "4165.83" "922.12"
[1] "Iteration:" "8" "Theta:" "8295.5" "0"
[1] "Iteration:" "9" "Theta:" "13497.65" "0"
[1] "Iteration:" "10" "Theta:" "18798.51" "0"
[1] "Iteration:" "11" "Theta:" "24464.08" "0"
[1] "Iteration:" "12" "Theta:" "11416.97" "0"
[1] "Iteration:" "13" "Theta:" "15184.66" "0"
[1] "Iteration:" "14" "Theta:" "21280.78" "0"
[1] "Iteration:" "15" "Theta:" "20079.34" "0"
[1] "Iteration:" "16" "Theta:" "21753.12" "0"
[1] "Iteration:" "17" "Theta:" "15461.88" "0"
[1] "Iteration:" "18" "Theta:" "16622.59" "0"
[1] "Iteration:" "19" "Theta:" "21829.12" "0"
[1] "Iteration:" "20" "Theta:" "0" "8673.05"
[1] "Iteration:" "21" "Theta:" "179.57" "10062.57"
[1] "Iteration:" "22" "Theta:" "851.22" "8750.5"
[1] "Iteration:" "23" "Theta:" "3861.07" "2978.94"
[1] "Iteration:" "24" "Theta:" "9205.44" "0"
[1] "Iteration:" "25" "Theta:" "15045.31" "0"
[1] "Iteration:" "26" "Theta:" "15221.25" "0"
[1] "Iteration:" "27" "Theta:" "22591.51" "0"
[1] "Iteration:" "28" "Theta:" "26538.09" "0"
[1] "Iteration:" "29" "Theta:" "0" "3191.93"
[1] "Iteration:" "30" "Theta:" "24.32" "5397.35"
[1] "Iteration:" "31" "Theta:" "130.59" "7869.76"
[1] "Iteration:" "32" "Theta:" "547.17" "8856.37"
[1] "Iteration:" "33" "Theta:" "2455.76" "5345.19"
[1] "Iteration:" "34" "Theta:" "7451.95" "33.24"
[1] "Iteration:" "35" "Theta:" "12677.86" "0"
[1] "Iteration:" "36" "Theta:" "18556.27" "0"
[1] "Iteration:" "37" "Theta:" "22523.37" "0"
[1] "Iteration:" "38" "Theta:" "17425.75" "0"
[1] "Iteration:" "39" "Theta:" "21327.84" "0"
[1] "Iteration:" "40" "Theta:" "21600.06" "0"
[1] "Iteration:" "41" "Theta:" "29564.68" "0"
[1] "Iteration:" "42" "Theta:" "0" "0"
[1] "Iteration:" "43" "Theta:" "0" "0"
[1] "Converged at Iteration:" "43"
[3] "Theta:" "0"
[5] "0" stat <- glma(fit = fit, W = W)
#qqplot
qq(stat[,4], main="Female Gene p-values")
| Version | Author | Date |
|---|---|---|
| 177257f | nklimko | 2022-12-21 |
Male
#read in p values
mReg <- fread("data/mRegress.txt")
#read in expression data
mMeans <- fread("data/mMeans.txt")
#create matrix of only gene expression, trims line and starvation
Y <- as.matrix(mMeans[,3:13577], row.names=1)
#dimensions and number of fixed effect genes
n <- dim(Y)[1]
p <- dim(Y)[2]
p_effect <- 525
#p_effect <- round(p / 15)
# add gene names to p val list
geneNames <- colnames(mMeans)[3:13577]
mReg <- mReg[, gene:=geneNames]
###sorted p values
# LOW pval
#pSort <- mReg[order(pvalList)]
#HIGH pval
pSort <- mReg[order(-pvalList)]
# fixed effect vector USELESS, must be matched to certain values
b <- c(rnorm(p_effect, mean=6), rep(0, p-p_effect))
#affix vector to sorted p values
pSort[,b:=b]
#restore sort order to id/alphabetical gene, matches expression data order
mFin <- pSort[order(id)]
# PROPER fixed effect vector PROPER with proper indexing
b <- mFin[,b]
#error is seeded rnorm, number of rows(lines)
e <- rnorm(n, 1, 0.25)
e <- rnorm(n)
#matrix multiplication of the data and p
y <- drop(Y%*%b) + e
###Create model for covariates to adjust for (only an intercept in our case)
mu <- rep(1, length(y))
names(mu) <- names(y)
###Compute transcriptomic relationship matrix (accounts for structure based on expression levels)
W <- scale(Y)
TRM <- tcrossprod(W)/ncol(W)
###Fit mixed model
fit <- greml(y = y, X = mu, GRM = list(TRM), verbose = TRUE)[1] "Iteration:" "1" "Theta:" "67.12" "66.26"
[1] "Iteration:" "2" "Theta:" "134.91" "129.78"
[1] "Iteration:" "3" "Theta:" "272.45" "248.79"
[1] "Iteration:" "4" "Theta:" "555.04" "456.14"
[1] "Iteration:" "5" "Theta:" "1147.56" "758.93"
[1] "Iteration:" "6" "Theta:" "2419.77" "995.89"
[1] "Iteration:" "7" "Theta:" "5131.9" "519.48"
[1] "Iteration:" "8" "Theta:" "9959.11" "0"
[1] "Iteration:" "9" "Theta:" "16310.79" "0"
[1] "Iteration:" "10" "Theta:" "20358.71" "0"
[1] "Iteration:" "11" "Theta:" "24474.35" "0"
[1] "Iteration:" "12" "Theta:" "13600.55" "0"
[1] "Iteration:" "13" "Theta:" "18941.17" "0"
[1] "Iteration:" "14" "Theta:" "28096.15" "0"
[1] "Iteration:" "15" "Theta:" "23638.18" "0"
[1] "Iteration:" "16" "Theta:" "29428.87" "0"
[1] "Iteration:" "17" "Theta:" "20912.7" "0"
[1] "Iteration:" "18" "Theta:" "24153.18" "0"
[1] "Iteration:" "19" "Theta:" "30225.63" "0"
[1] "Iteration:" "20" "Theta:" "20537.07" "0"
[1] "Iteration:" "21" "Theta:" "25064.16" "0"
[1] "Iteration:" "22" "Theta:" "27891.38" "0"
[1] "Iteration:" "23" "Theta:" "29893.94" "0"
[1] "Iteration:" "24" "Theta:" "34179.96" "0"
[1] "Iteration:" "25" "Theta:" "0" "6389.34"
[1] "Iteration:" "26" "Theta:" "165" "8818.54"
[1] "Iteration:" "27" "Theta:" "714.36" "9334.69"
[1] "Iteration:" "28" "Theta:" "2253.96" "6761.17"
[1] "Iteration:" "29" "Theta:" "6603.69" "1212.43"
[1] "Iteration:" "30" "Theta:" "13450.58" "0"
[1] "Iteration:" "31" "Theta:" "19797.88" "0"
[1] "Iteration:" "32" "Theta:" "25555.02" "0"
[1] "Iteration:" "33" "Theta:" "0" "6838.35"
[1] "Iteration:" "34" "Theta:" "189.01" "9140.41"
[1] "Iteration:" "35" "Theta:" "800.24" "9276.18"
[1] "Iteration:" "36" "Theta:" "2500.69" "6358.49"
[1] "Iteration:" "37" "Theta:" "7248.68" "588.32"
[1] "Iteration:" "38" "Theta:" "13664.31" "0"
[1] "Iteration:" "39" "Theta:" "20969.31" "0"
[1] "Iteration:" "40" "Theta:" "26751.79" "0"
[1] "Iteration:" "41" "Theta:" "0" "7381.46"
[1] "Iteration:" "42" "Theta:" "220.22" "9477.46"
[1] "Iteration:" "43" "Theta:" "907.81" "9155.03"
[1] "Iteration:" "44" "Theta:" "2809.38" "5872.14"
[1] "Iteration:" "45" "Theta:" "8016.1" "0"
[1] "Iteration:" "46" "Theta:" "13956.18" "0"
[1] "Iteration:" "47" "Theta:" "22143.48" "0"
[1] "Iteration:" "48" "Theta:" "30798.36" "0"
[1] "Iteration:" "49" "Theta:" "25500.08" "0"
[1] "Iteration:" "50" "Theta:" "28702.26" "0"
[1] "Iteration:" "51" "Theta:" "29545.3" "0"
[1] "Iteration:" "52" "Theta:" "21718.96" "0"
[1] "Iteration:" "53" "Theta:" "29634.62" "0"
[1] "Iteration:" "54" "Theta:" "34044.94" "0"
[1] "Iteration:" "55" "Theta:" "24358.5" "0"
[1] "Iteration:" "56" "Theta:" "29489.91" "0"
[1] "Iteration:" "57" "Theta:" "0" "0"
[1] "Iteration:" "58" "Theta:" "0" "0"
[1] "Converged at Iteration:" "58"
[3] "Theta:" "0"
[5] "0" stat <- glma(fit = fit, W = W)
#qqplot
qq(stat[,4], main="Male Gene p-values")
| Version | Author | Date |
|---|---|---|
| 177257f | nklimko | 2022-12-21 |
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] qgg_1.1.1 qqman_0.1.8 cowplot_1.1.1 ggplot2_3.3.5
[5] data.table_1.14.2 dplyr_1.0.8 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 lattice_0.20-45 getPass_0.2-2 ps_1.6.0
[5] assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.29 utf8_1.2.2
[9] R6_2.5.1 MatrixModels_0.5-1 evaluate_0.15 coda_0.19-4
[13] highr_0.9 httr_1.4.2 pillar_1.7.0 rlang_1.0.4
[17] rstudioapi_0.13 SparseM_1.81 whisker_0.4 callr_3.7.0
[21] jquerylib_0.1.4 Matrix_1.5-3 rmarkdown_2.16 splines_4.0.3
[25] statmod_1.4.37 stringr_1.4.0 munsell_0.5.0 compiler_4.0.3
[29] httpuv_1.6.5 xfun_0.30 pkgconfig_2.0.3 mcmc_0.9-7
[33] htmltools_0.5.2 tidyselect_1.1.2 tibble_3.1.6 fansi_1.0.3
[37] calibrate_1.7.7 crayon_1.5.1 withr_2.5.0 later_1.3.0
[41] MASS_7.3-56 grid_4.0.3 jsonlite_1.8.0 gtable_0.3.0
[45] lifecycle_1.0.1 DBI_1.1.2 git2r_0.30.1 magrittr_2.0.3
[49] scales_1.2.0 cli_3.3.0 stringi_1.7.6 fs_1.5.2
[53] promises_1.2.0.1 bslib_0.3.1 ellipsis_0.3.2 generics_0.1.2
[57] vctrs_0.4.1 tools_4.0.3 glue_1.6.2 purrr_0.3.4
[61] parallel_4.0.3 processx_3.5.3 fastmap_1.1.0 survival_3.3-1
[65] yaml_2.3.5 colorspace_2.0-3 knitr_1.38 sass_0.4.1
[69] quantreg_5.94 MCMCpack_1.6-3