init v3 HTRsim

src/v3/HTRsim/DESCRIPTION

+Package: HTRsim
+Title: Hightroughtput RNA-seq simulation
+Version: 0.3
+Authors@R: person('Duvermy', 'Arnaud', email = 'arnaud.duvermy@ens-lyon.Fr', role = c('aut', 'cre'))
+Description: Hightroughtput RNA-seq simulation.
+License: GPL-3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.2
+Depends: 
+    tidyverse
+Imports: 
+    S4Vectors,
+    stats,
+    stringr,
+    tidyr

src/v3/HTRsim/HTRsim.Rproj

+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

src/v3/HTRsim/NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(extractionDDS)
+import(S4Vectors)
+import(stats)
+import(tidyr)

src/v3/HTRsim/R/extractionFromDDS.R

+#' Extract beta distribution from DESEQ2 object
+#'
+#' @param dds_obj a DESEQ2 object
+#' @import S4Vectors
+#' @import tidyr
+#' @import stats
+#' @return a list containing 1- mean and sd of BetaG 2- mean and sd of BetaE 3- mean and sd of BetaGE 5- mean and sd of gene dispersion
+#' @export
+#'
+#' @examples
+extractionDDS <-  function(dds_obj){
+  ## Beta
+  dds.mcols = S4Vectors::mcols(dds_obj, use.names=TRUE)
+  beta0 <- dds.mcols$Intercept
+  betaG <- dds.mcols$genotype_RM11_vs_GSY147
+  betaE <- dds.mcols$environment_treated_vs_untreated
+  betaGE <- dds.mcols$genotypeRM11.environmenttreated
+  beta.dtf = cbind(beta0,betaG,betaE,betaGE) %>% as.data.frame() %>% tidyr::drop_na()
+
+  ## Dispersion
+  gene_disp = dds.mcols$dispersion %>% stats::na.omit()
+
+
+  return(list(beta = beta.dtf,
+              gene_dispersion = gene_disp,
+              beta0.mean = mean(beta.dtf$beta0,  na.rm = T), beta0.sd = sd(beta.dtf$beta0,  na.rm = T) ,
+              betaG.mean = mean(beta.dtf$betaG,  na.rm = T), betaG.sd = sd(beta.dtf$betaG,  na.rm = T) ,
+              betaE.mean = mean(beta.dtf$betaE, na.rm = T)  , betaE.sd = sd(beta.dtf$betaE,  na.rm = T) ,
+              betaGE.mean =  mean(beta.dtf$betaGE, na.rm = T)  , betaGE.sd = sd(beta.dtf$betaGE,  na.rm = T),
+              gene_disp.mean = mean(gene_disp, na.rm = T) ,  gene_disp.sd = sd(gene_disp, na.rm = T)))
+
+}

src/v3/HTRsim/devtools_history.R

+usethis::use_build_ignore("devtools_history.R")
+usethis::use_package('tidyverse', type = "depends")
+usethis::use_package('stats')
+usethis::use_package('tidyr')
+usethis::use_package("stringr")
+usethis::use_package("S4Vectors")

src/v3/HTRsim/man/extractionDDS.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/extractionFromDDS.R
+\name{extractionDDS}
+\alias{extractionDDS}
+\title{Extract beta distribution from DESEQ2 object}
+\usage{
+extractionDDS(dds_obj)
+}
+\arguments{
+\item{dds_obj}{a DESEQ2 object}
+}
+\value{
+a list containing 1- mean and sd of BetaG 2- mean and sd of BetaE 3- mean and sd of BetaGE 5- mean and sd of gene dispersion
+}
+\description{
+Extract beta distribution from DESEQ2 object
+}