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#'
#' @title Get the contents of a data folder
#'
#' @description Get the cel files of the specified dataSetName
#'
#' @param dataSetName The name of a data-set folder
#' @param chipType The name of the used chip
#'
#' @return The filenames of all the files in rawData/dataSetName/chipType
#'
#' @details If chipType is not provided, the function returns the files for the first chip (in the alphabetic order).
#'
#' @author Quentin Grimonprez
#'
#' @export
getListOfFiles=function(dataSetName,chipType)
{
if(!("annotationData"%in%list.files()))
stop("There is no annotationData folder in the current architecture.")
if(!("rawData"%in%list.files()))
stop("There is no rawData folder in the current architecture.")
#dataSetName
if(missing(dataSetName))
stop("dataSetName is missing")
if(!is.character(dataSetName))
stop("dataSetName must be a string.")
#chipType
if(missing(chipType))
chipType=list.files(paste0("rawData/",dataSetName,"/"))[1]
if(!is.character(chipType))
stop("chipType must be a string.")
files=list.files(paste0("rawData/",dataSetName,"/",chipType,"/"))
withoutextension=gsub(".CEL$","",files)
withoutextension=gsub(".cel$","",withoutextension)
return(withoutextension)
}
#'
#' Create a folder in "annotationData/chipTypes" and copy the specified files in this folder.
#'
#' @title Add a new chip type to the existing aroma architecture
#'
#' @param chipType Name of the new chiptype to add.
#' @param chipPath Path to the files to add.
#' @param verbose Print additionnal information
#'
#' @author Quentin Grimonprez
#'
#' @export
addChipType=function(chipType,chipPath,verbose=TRUE)
{
#check arguments
if(missing(chipPath))
stop("chipPath is missing.")
if(missing(chipType))
stop("chipType is missing.")
if(!is.character(chipPath))
stop("dataSetName must be a string.")
if(!is.character(chipType))
stop("chipType must be a string.")
if(!("annotationData"%in%list.files()))
stop("There is no annotationData folder in the current architecture.")
existingChip=list.files("annotationData/chipTypes")
if(chipType%in%existingChip)
stop(paste0("A ",chipType," folder already exits."))
if(!file.exists(paste0("./annotationData/chipTypes/",chipType)))
{
dir.create(paste0("./annotationData/chipTypes/",chipType),recursive=TRUE)
#test existence of the created folders
ok2=file.access(paste0("./annotationData/chipTypes/",chipType), mode = 0)
if(ok2 != 0)
stop(paste0("Can not create \"","./annotationData/chipTypes/",chipType,"\" folder."))
else
{
if(verbose)
cat(gsub("//","/",paste0("Folder \"","./annotationData/chipTypes/",chipType,"\" created.")),"\n")
}
}
copyChipFiles(chipPath,chipType,".",TRUE)
}
#'
#' Create a folder in "rawData" and copy the specified files in this folder.
#'
#' @title Add a new data-set to the existing aroma architecture
#'
#' @param dataSetName Name of the data-set folder to create.
#' @param dataPath Path of the folder containing the data CEL files.
#' @param chipType Name of the used chip.
#' @param verbose Print additionnal information.
#'
#' @author Quentin Grimonprez
#'
#' @export
addData=function(dataSetName,dataPath,chipType,verbose=TRUE)
{
#check arguments
if(missing(dataSetName))
stop("dataSetName is missing.")
if (missing(dataPath))
stop("dataPath is missing")
if(missing(chipType))
stop("chipType is missing.")
if(!is.character(dataSetName))
stop("dataSetName must be a string.")
if(!is.character(dataPath))
stop("dataSetName must be a string.")
if(!is.character(chipType))
stop("chipType must be a string.")
if(!("annotationData"%in%list.files()))
stop("There is no annotationData folder in the current architecture.")
if(!("rawData"%in%list.files()))
stop("There is no rawData folder in the current architecture.")
existingChip=list.files("annotationData/chipTypes")
if(!(chipType%in%existingChip))
stop(paste0("The ",chipType," folder does not exist."))
#create rawData
if(!file.exists(paste0("./rawData/",dataSetName,"/",chipType)))
{
dir.create(paste0("./rawData/",dataSetName,"/",chipType),recursive=TRUE)
ok1=file.access(paste0("./rawData/",dataSetName,"/",chipType), mode = 0)
if(ok1 != 0)
stop(paste0("Can not create \"",".","/rawData/",dataSetName,"/",chipType,"\" folder."))
else
{
if(verbose)
cat(gsub("//","/",paste0("Folder \"",".","/rawData/",dataSetName,"/",chipType,"\" created.")),"\n")
}
}
copyDataFiles(dataSetName,dataPath,chipType,".",TRUE)
}
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