#R
# by WEW
# this are some function to copy RMD files and preprare envs.
.scriptCopyHelperVec <- function(runscripts, workdir = getwd() ){
for(scripts in runscripts){
src_script <- file.path( find.package("SRMService") , scripts )
dest_script <- file.path(workdir ,basename(scripts))
message("copy ", src_script, " to ", dest_script)
if(!file.copy(src_script , dest_script)){
warning(paste("could not copy script file. Does file already exist?", dest_script, sep=" "))
}
}
message(paste("your working directory now should contain ", length(runscripts) , "new files :\n",sep=" "))
res <- NULL
for(script in runscripts){
message( basename(script) )
res <- c(res, basename(script) )
}
}
#' copies the RMD and Run files for 2 grp analysis based on MQ (MaxQuant) in your working directory
#' - ideally the txt directory of your MQ session.
#'
#' Please see the Run_QuantTwoGroupAnalysis.R for more details
#'
#' @export
#' @examples
#'
#' \dontrun{
#' SRMService::RMD_MQ_Quant_2GrpAnalysis()
#' }
#' @param workdir specify working directory
#'
RMD_MQ_Quant_2GrpAnalysis <- function(workdir = getwd()){
.scriptCopyHelperVec(c("/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R",
"/doc/Grp2Analysis.Rmd",
"/doc/bibliography.bib",
"/doc/Grp2Analysis_MissingInOneCondition.Rmd",
"/doc/Empty.Rmd"), workdir = workdir )
}
#' copies the RMD and Run files for 2 grp analysis based on a PD (protein discoverer) in your working directory.
#'
#' Please see the Run_QuantTwoGroupAnalysis.R for more details
#'
#' @export
#' @examples
#' \dontrun{
#' SRMService::RMD_PD_Quant_2GrpAnalysis()
#' }
#' @param workdir specify working directory
#'
RMD_PD_Quant_2GrpAnalysis <- function(workdir= getwd()){
.scriptCopyHelperVec(c("/RunScripts/Run_PD_QuantTwoGroupAnalysis.R",
"/doc/Grp2Analysis.Rmd",
"/doc/bibliography.bib",
"/doc/Grp2Analysis_Empty.Rmd_t",
"/doc/Grp2Analysis_MissingInOneCondtion.Rmd_t"), workdir = workdir )
}
#' copies the RMD and Run files for the QuantQCReport in your working directory.
#'
#' Please see the Run_QuantQCReport.R for more details
#'
#' @param workdir specify working directory
#' @export
#' @examples
#' \dontrun{
#' SRMService::RMD_MQ_Quant_QCReport()
#' }
RMD_MQ_Quant_QCReport <- function(workdir = getwd()){
.scriptCopyHelperVec(c("/RunScripts/Run_QuantQCReport.R","/reports/QCReport.Rmd"), workdir = workdir )
}
#' Copies the RMD and Run files for variable selection into your working directory.
#'
#' Please see the Run_QuantTwoGroupAnalysis.R for more details
#'
#' @export
#'
#' @param workdir specify working directory
#'
RMD_VarSelection <- function(workdir = getwd()){
.scriptCopyHelperVec(c("/RunScripts/RUN_VarSelection_Multinomial.R",
"/reports/VariableSelection_MultinomialLasso.Rmd",
"/RunScripts/RUN_VarSelection_GLM.R",
"/reports/VariableSelection_ROCSingleProtein.Rmd",
"/reports/VariableSelection_GLM.Rmd"
), workdir =workdir )
}
#' Copies the RMD and Run R file for Library generation your working directory.
#'
#' Please see the Run_specLProzor.R file in the working directory
#' for more details
#'
#' @export
#' @param workdir specify working directory
#'
RMD_LibraryGen_specLProzor <- function(workdir = getwd()){
.scriptCopyHelperVec(c("/RunScripts/Run_specLWithProzor.R","/reports/specLWithProzor.Rmd"), workdir = workdir )
}
#' Copies the Rnw file and Run R file for old 1To1 QC into your working directory.
#'
#' Please see the Run_1To1_oldStyle.R file in your working directory,
#' for more details
#'
#' @export
#' @param workdir specify working directory
#'
RMD_QC1To1_Old <- function(workdir = getwd(), minimal = TRUE){
if(!minimal){
.scriptCopyHelperVec(c("/OneToOneAnalysis/Run_1To1_oldStyle.R",
"/OneToOneAnalysis/fgcz_MQ_QC_report.Rnw",
"/OneToOneAnalysis/images/LFQ_QC_workflow.pdf",
"/OneToOneAnalysis/images/Sweave.sty"), workdir = workdir)
}else{
.scriptCopyHelperVec(c("/OneToOneAnalysis/fgcz_MQ_QC_report.Rnw",
"/OneToOneAnalysis/images/LFQ_QC_workflow.pdf",
"/OneToOneAnalysis/images/Sweave.sty"), workdir = workdir)
}
}
.RMD_QC1To1_Old <- function(workdir = getwd(), minimal = TRUE){
if(!minimal){
.scriptCopyHelperVec(c("/OneToOneAnalysis/Run_1To1_oldStyle.R",
"/OneToOneAnalysis/MQ_sampleQC_overview.Rnw",
"/OneToOneAnalysis/images/LFQ_QC_workflow.pdf",
"/OneToOneAnalysis/images/Sweave.sty"), workdir = workdir)
}else{
.scriptCopyHelperVec(c("/OneToOneAnalysis/MQ_sampleQC_overview.Rnw",
"/OneToOneAnalysis/images/LFQ_QC_workflow.pdf",
"/OneToOneAnalysis/images/Sweave.sty"), workdir = workdir)
}
}
#' Copies the Rnw file and Run R file for the SRM QC and normalization.
#'
#' Please see the Run_1To1_oldStyle.R file in your working directory,
#' for more details
#'
#' @export
#' @param workdir specify working directory
#'
RMD_SRM_QC_Normalization <- function(workdir = getwd()){
.scriptCopyHelperVec(c("/reports/SRM_NormalizeByProteins.Rmd",
"/reports/SRM_PeptideProteinQC.Rmd",
"/RunScripts/RUN_SRMPeptideProteinQC.R"), workdir = workdir)
}
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