R/getProbePositionsDf.R

In markrobinsonuzh/Repitools: Epigenomic tools

#setOldClass("AffymetrixCdfFile")
#
#setGeneric("getProbePositionsDf", function(cdf, ...)
#           {standardGeneric("getProbePositionsDf")})
#
#setMethod("getProbePositionsDf", "AffymetrixCdfFile",
#    function(cdf, chrs = NULL, ..., verbose = TRUE)
#{
#    ind <- getCellIndices(cdf, ..., useNames = FALSE, unlist = TRUE, verbose = verbose)
#    acp <- AromaCellPositionFile$byChipType(getChipType(cdf))
#    ch <- acp[ind,1,drop=TRUE]
#    sp <- acp[ind,2,drop=TRUE]
#    if(is.null(chrs)) chrs <- ch else chrs <- chrs[ch]
#
#    data.frame(chr = chrs,
#               position = sp,
#               index = ind,
#               stringsAsFactors = FALSE)
#})