R/list_illumina_manifest_files.R

In drmjc/lumidat: Methods for importing Illumina gene expression iDAT files

#' List the available Illumina manifest files.
#' 
#' Note, you must have an internet connection for this to work.
#'
#' @param all logical: if \code{TRUE}, then report all current and archived manifest names;
#'  default=\code{FALSE}, where only the current manifest names are reported
#' @param verbose logical: if \code{TRUE} prints info when downloading the HTML pages from Illumina.
#' 
#' @return a character vector of manifest names
#' 
#' @author Mark Cowley, 2012-10-14
#' @export
#' @seealso \code{\link{download_illumina_manifest_file}}
#' @references 
#' [1] \url{http://www.switchtoi.com/annotationfiles.ilmn} \cr
#' [2] \url{http://www.switchtoi.com/annotationprevfiles.ilmn} \cr
#' @examples
#' \dontrun{
#' #
#' # output as of 2012-10-14
#' #
#' list_illumina_manifest_files()
#' #  [1] "HumanHT-12_V4_0_R2_15002873_B_WGDASL"
#' #  [2] "HumanHT-12_V4_0_R2_15002873_B"       
#' #  [3] "HumanHT-12_V4_0_R1_15002873_B"       
#' #  [4] "HumanHT-12_V3_0_R2_11283641_A"       
#' #  [5] "HumanHT-12_V3_0_R3_11283641_A"       
#' #  [6] "HumanRef-8_V2_0_R4_11223162_A"       
#' #  [7] "HUMANREF-8_V3_0_R1_11282963_A_WGDASL"
#' #  [8] "HumanRef-8_V3_0_R2_11282963_A"       
#' #  [9] "HumanRef-8_V3_0_R3_11282963_A"       
#' # [10] "HumanWG-6_V2_0_R4_11223189_A"        
#' # [11] "HumanWG-6_V3_0_R2_11282955_A"        
#' # [12] "HumanWG-6_V3_0_R3_11282955_A"        
#' # [13] "MouseRef-8_V1_1_R4_11234312_A"       
#' # [14] "MouseRef-8_V2_0_R2_11278551_A"       
#' # [15] "MouseRef-8_V2_0_R3_11278551_A"       
#' # [16] "MouseWG-6_V1_1_R4_11234304_A"        
#' # [17] "MouseWG-6_V2_0_R2_11278593_A"        
#' # [18] "MouseWG-6_V2_0_R3_11278593_A"        
#' # [19] "RatRef-12_V1_0_R5_11222119_A"        
#' # [20] "HumanMI_V1_R2_XS0000122-MAP"         
#' # [21] "HumanMI_V2_R0_XS0000124-MAP"         
#' # [22] "MouseMI_V1_R2_XS0000127-MAP"         
#' # [23] "MouseMI_V2_R0_XS0000129-MAP"
#' 
#' list_illumina_manifest_files(all=TRUE)
#' # another 20 arrays
#' }
list_illumina_manifest_files <- function(all=FALSE, verbose=FALSE) {
	res <- .parse_illumina_manifest_html(verbose=verbose)
	if( !all ) res <- res[res$current, ]
	res$Name
}