From 816e046c30860e18d83604709706e2f5b64ab198 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Sun, 4 Dec 2022 19:47:19 +0100
Subject: [PATCH] init v3 HTRsim
---
src/v3/HTRsim/DESCRIPTION | 16 +++++++++++++++
src/v3/HTRsim/HTRsim.Rproj | 22 ++++++++++++++++++++
src/v3/HTRsim/NAMESPACE | 6 ++++++
src/v3/HTRsim/R/extractionFromDDS.R | 32 +++++++++++++++++++++++++++++
src/v3/HTRsim/devtools_history.R | 6 ++++++
src/v3/HTRsim/man/extractionDDS.Rd | 17 +++++++++++++++
6 files changed, 99 insertions(+)
create mode 100644 src/v3/HTRsim/DESCRIPTION
create mode 100644 src/v3/HTRsim/HTRsim.Rproj
create mode 100644 src/v3/HTRsim/NAMESPACE
create mode 100644 src/v3/HTRsim/R/extractionFromDDS.R
create mode 100644 src/v3/HTRsim/devtools_history.R
create mode 100644 src/v3/HTRsim/man/extractionDDS.Rd
diff --git a/src/v3/HTRsim/DESCRIPTION b/src/v3/HTRsim/DESCRIPTION
new file mode 100644
index 0000000..e4a9261
--- /dev/null
+++ b/src/v3/HTRsim/DESCRIPTION
@@ -0,0 +1,16 @@
+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
diff --git a/src/v3/HTRsim/HTRsim.Rproj b/src/v3/HTRsim/HTRsim.Rproj
new file mode 100644
index 0000000..69fafd4
--- /dev/null
+++ b/src/v3/HTRsim/HTRsim.Rproj
@@ -0,0 +1,22 @@
+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
diff --git a/src/v3/HTRsim/NAMESPACE b/src/v3/HTRsim/NAMESPACE
new file mode 100644
index 0000000..b57165e
--- /dev/null
+++ b/src/v3/HTRsim/NAMESPACE
@@ -0,0 +1,6 @@
+# Generated by roxygen2: do not edit by hand
+
+export(extractionDDS)
+import(S4Vectors)
+import(stats)
+import(tidyr)
diff --git a/src/v3/HTRsim/R/extractionFromDDS.R b/src/v3/HTRsim/R/extractionFromDDS.R
new file mode 100644
index 0000000..8079ccf
--- /dev/null
+++ b/src/v3/HTRsim/R/extractionFromDDS.R
@@ -0,0 +1,32 @@
+#' 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)))
+
+}
diff --git a/src/v3/HTRsim/devtools_history.R b/src/v3/HTRsim/devtools_history.R
new file mode 100644
index 0000000..b82eb31
--- /dev/null
+++ b/src/v3/HTRsim/devtools_history.R
@@ -0,0 +1,6 @@
+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")
diff --git a/src/v3/HTRsim/man/extractionDDS.Rd b/src/v3/HTRsim/man/extractionDDS.Rd
new file mode 100644
index 0000000..e17f405
--- /dev/null
+++ b/src/v3/HTRsim/man/extractionDDS.Rd
@@ -0,0 +1,17 @@
+% 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
+}
--
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