Nothing
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# TODO LIST
# TODO: ...
################################################################################
# CHANGE LOG (last 20 changes)
# 29.08.2015: Added importFrom.
# 15.12.2014: Changed parameter names to format: lower.case
# 30.09.2014: Check if package is loaded to avoid error in path.package.
# 01.10.2013: First version.
#' @title Get Allele Frequency Database
#'
#' @description
#' Gives access to allele frequency databases.
#'
#' @details
#' The function provides access to allele frequency databases stored in
#' the file database.txt in the package directory.
#' It returns the specified allele frequency database.
#'
#' @param db.name.or.index string or integer specifying the database.
#' If NULL a vector of available databases is returned.
#' @param debug logical indicating printing debug information.
#'
#' @return data.frame with allele frequency database information.
#' If no matching database or database index is found NA is returned.
#' If the database was not found NULL is returned.
#'
#' @keywords internal
#'
#' @export
#'
#' @importFrom utils read.delim
#'
#' @examples
#' # Show available allele frequency databases.
#' getDb()
getDb <- function(db.name.or.index = NULL, debug = FALSE) {
if (debug) {
print(paste("IN:", match.call()[[1]]))
}
.separator <- .Platform$file.sep # Platform dependent path separator.
# LOAD DATABASE INFO #######################################################
# Get package path.
if (require(strvalidator)) {
packagePath <- path.package("strvalidator", quiet = FALSE)
} else {
warning("Package path for strvalidator not found!")
return(NULL)
}
subFolder <- "extdata"
fileName <- "database.txt"
# Create complete file path.
filePath <- paste(packagePath, subFolder, fileName, sep = .separator)
.db <- read.delim(
file = filePath, header = TRUE, sep = "\t", quote = "\"",
dec = ".", fill = TRUE, stringsAsFactors = FALSE
)
# Available databases. Must match else if construct.
databases <- unique(.db$Database)
# Check if NULL
if (is.null(db.name.or.index)) {
db <- databases
# String provided.
} else {
# Check if number or string.
if (is.numeric(db.name.or.index)) {
# Set index to number.
index <- db.name.or.index
} else {
# Find matching database index (case insensitive)
index <- match(toupper(db.name.or.index), toupper(databases))
}
# No matching database.
if (is.na(index)) {
db <- NA
# Assign matching database information.
} else {
db <- .db[.db$Database == databases[index], ]
}
}
return(db)
}
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