---
Author: "Amin Haghani"
Paper: "DNA Methylation Networks Underlying Mammalian Traits"
Authors: "Amin Haghani1, 2 †*; Caesar Z. Li3, 4 †; Todd R. Robeck5; Joshua Zhang1; Ake T. Lu1, 2; Julia Ablaeva6; Victoria A. Acosta-Rodríguez7; Danielle M. Adams8; Abdulaziz N. Alagaili9, 10; Javier Almunia11; Ajoy Aloysius12; Nabil M.S. Amor13; Reza Ardehali14; Adriana Arneson15, 16; C. Scott Baker17; Gareth Banks18; Katherine Belov19; Nigel C. Bennett20; Peter Black21; Daniel T. Blumstein22, 23; Eleanor K. Bors17; Charles E. Breeze24; Robert T. Brooke25; Janine L. Brown26; Gerald Carter27; Alex Caulton28, 29; Julie M. Cavin30; Lisa Chakrabarti31; Ioulia Chatzistamou32; Andreas S. Chavez27, 33; Hao Chen34; Kaiyang Cheng35; Priscila Chiavellini36; Oi-Wa Choi37, 38; Shannon Clarke28; Joseph A. Cook39; Lisa N. Cooper40; Marie-Laurence Cossette41; Joanna Day42; Joseph DeYoung37, 38; Stacy Dirocco43; Christopher Dold44; Jonathan L. Dunnum39; Erin E. Ehmke45; Candice K. Emmons46; Stephan Emmrich6; Ebru Erbay47, 48, 49; Claire Erlacher-Reid43; Chris G. Faulkes50, 51; Zhe Fei3, 52; Steven H. Ferguson53, 54; Carrie J. Finno55; Jennifer E. Flower56; Jean-Michel Gaillard57; Eva Garde58; Livia Gerber59, 60; Vadim N. Gladyshev61; Rodolfo G. Goya36; Matthew J Grant62; Carla B. Green7; M. Bradley Hanson46; Daniel W. Hart20; Martin Haulena63; Kelsey Herrick64; Andrew N. Hogan65; Carolyn J. Hogg19; Timothy A. Hore66; Taosheng Huang67; Juan Carlos Izpisua Belmonte2; Anna J. Jasinska37, 68, 69; Gareth Jones70; Eve Jourdain71; Olga Kashpur72; Harold Katcher73; Etsuko Katsumata74; Vimala Kaza75; Hippokratis Kiaris76; Michael S. Kobor77; Pawel Kordowitzki78; William R. Koski79; Michael Krützen60; Soo Bin Kwon16, 15; Brenda Larison22, 80; Sang-Goo Lee61; Marianne Lehmann36; Jean-François Lemaître57; Andrew J. Levine81; Xinmin Li82; Cun Li83, 84; Andrea R. Lim1; David T.S. Lin85; Dana M. Lindemann43; Schuyler W.  Liphardt86; Thomas J. Little87; Nicholas Macoretta6; Dewey Maddox88; Craig O. Matkin89; Julie A. Mattison90; Matthew McClure91; June Mergl92; Jennifer J. Meudt93; Gisele A. Montano5; Khyobeni Mozhui94; Jason Munshi-South95; William J. Murphy96, 97; Asieh Naderi76; Martina Nagy98; Pritika Narayan62; Peter W. Nathanielsz83, 84; Ngoc B. Nguyen14; Christof Niehrs99, 100; Batsaikhan Nyamsuren101; Justine K. O'Brien42; Perrie O'Tierney Ginn72; Duncan T Odom102, 103; Alexander G. Ophir104; Steve Osborn105; Elaine A. Ostrander65; Kim M. Parsons46; Kimberly C. Paul81; Amy B. Pedersen87; Matteo Pellegrini106; Katharina J. Peters60, 107; Jessica L. Petersen108; Darren W. Pietersen109; Gabriela M. Pinho22; Jocelyn Plassais65; Jesse R. Poganik61; Natalia A. Prado110, 26; Pradeep Reddy111, 2; Benjamin Rey57; Beate R. Ritz112, 113, 81; Jooke Robbins114; Magdalena Rodriguez115; Jennifer Russell105; Elena Rydkina6; Lindsay L. Sailer104; Adam B. Salmon116; Akshay Sanghavi73; Kyle M. Schachtschneider117, 118, 119; Dennis Schmitt120; Todd Schmitt64; Lars Schomacher99; Lawrence B. Schook117, 121; Karen E. Sears22; Ashley W. Seifert12; Aaron B.A. Shafer122; Anastasia V. Shindyapina61; Melanie Simmons45; Kavita Singh123; Ishani Sinha22; Jesse Slone67; Russel G. Snell62; Elham Soltanmohammadi76; Matthew L. Spangler108; Maria Spriggs21; Lydia Staggs43; Nancy Stedman21; Karen J. Steinman124; Donald T Stewart125; Victoria J. Sugrue66; Balazs Szladovits126; Joseph S. Takahashi7, 127; Masaki Takasugi6; Emma C. Teeling128; Michael J. Thompson106; Bill Van Bonn129; Sonja C. Vernes130, 131; Diego Villar132; Harry V. Vinters133; Ha Vu15, 16; Mary C. Wallingford72; Nan Wang37, 38; Gerald S. Wilkinson8; Robert W. Williams134; Qi Yan3, 2; Mingjia Yao3; Brent G. Young54; Bohan Zhang61; Zhihui Zhang6; Yang Zhao6; Peng Zhao14, 135; Wanding Zhou136, 137; Joseph A. Zoller3; Jason Ernst15, 16; Andrei Seluanov138; Vera Gorbunova138; X. William Yang37, 38; Ken Raj139; Steve Horvath1, 2 *"
Date: "07-24-2023"
output: html_document
---

```{r libraries, message=FALSE}
library(easypackages)
libraries("readxl", "psych", "tidyr", "dplyr","gplots", "RColorBrewer","limma", "ggplot2", "metap", "anRichment", "clusterProfiler", "RColorBrewer", "ggstatsplot", "gridExtra", "ggupset", "psych", "corrplot", "limma", "edgeR", "gridExtra", "ggupset", "ggrepel", "data.table", "stringr")
```

```{r}

samplesNoMars <- readRDS("samples.RDS")
bValsNoMars <- readRDS("DNAmDataNoMarsupials.RDS")

multiSampels <- samplesNoMars %>% group_split(Order)
names(multiSampels) <- sapply(multiSampels, function(x){x$Order[1]})
multiSampels <- plyr::compact(plyr::llply(multiSampels, function(x){
  if(nrow(x)<3){x <- NULL}
  return(x)
}))

i <- which(names(multiSampels)=="Primates")
multiSampels <- multiSampels[c(i, 1:(i-1), (i+1):length(multiSampels))]


multiSampels <- plyr::llply(multiSampels, function(x){
  bval <- bValsNoMars %>% dplyr::select(x$Basename)
  bval <- list(data = t(bval))
})



mp = modulePreservation(multiSampels, multiColor = list("Primates" = mergedColors), nPermutations = 20)

saveRDS(mp, "model preservation no Marsupials.RDS")

result <- rbindlist(lapply(2:length(mp$preservation$Z$ref.Primates), function(x){
  dat <- mp$preservation$Z$ref.Primates[[x]]
  a <- data.frame(t(dat$Zsummary.pres))
  names(a) <- rownames(a)
  return(a)
}))

colnames(result) <- rownames(mp[[2]][[2]][[1]][[2]])
result <- result %>% mutate(Order = as.character(names(multiSampels)[-1])) %>% tibble::column_to_rownames(var = "Order")

```

```{r}

samples <- readRDS("samples.RDS")
bVals <- readRDS("DNAmDataAll.RDS")

multiSampels <- samples %>% group_split(Order)
names(multiSampels) <- sapply(multiSampels, function(x){x$Order[1]})
multiSampels <- plyr::compact(plyr::llply(multiSampels, function(x){
  if(nrow(x)<3){x <- NULL}
  return(x)
}))

i <- which(names(multiSampels)=="Primates")
multiSampels <- multiSampels[c(i, 1:(i-1), (i+1):length(multiSampels))]


multiSampels <- plyr::llply(multiSampels, function(x){
  bval <- bVals %>% dplyr::select(x$Basename)
  bval <- list(data = t(bval))
})



mp = modulePreservation(multiSampels, multiColor = list("Primates" = mergedColors), nPermutations = 20)

saveRDS(mp, "model preservation all samples.RDS")

result <- rbindlist(lapply(2:length(mp$preservation$Z$ref.Primates), function(x){
  dat <- mp$preservation$Z$ref.Primates[[x]]
  a <- data.frame(t(dat$Zsummary.pres))
  names(a) <- rownames(a)
  return(a)
}))

colnames(result) <- rownames(mp[[2]][[2]][[1]][[2]])
result <- result %>% mutate(Order = as.character(names(multiSampels)[-1])) %>% tibble::column_to_rownames(var = "Order")

```