"readallf"<-
function(fn, prefix = "")
{
#     use "File Save AS" to download this ascii file (" readin.txt")
#     use "File Save AS" to download DATA BASE as ascii file "ALL.txt"
# run Splus and 
# > source("readin.txt")
# > ls() and you should see this function				
# readallf - read in dataset(s) in 14 X 4 ascii format w/ Ids
#             Returns an S+ matrix where a row represents a patients
#             data
#Input
#  fn - ascii file name
#  prefix - directory where ascii file stored
# 
# Example:
#  readallf("ALL.txt","/usr2/users/home/datasets/")
#  (note - S+ matrices "bedata" & "nedata" automatically generated 
#          no need for assignment operator "<-" )
#create list for "what" arguement to scan function
#
	whatarg <- vector("list", 57)	# create NULL list of length 57
	whatarg[1] <- ""	#assign first value character data (IDs)
	whatarg[2:57] <- 0	# assign remaining values numeric data
#
#read in file, stored as list
#
	filename <- paste(prefix, fn, sep = "")
	list.x <- scan(file = filename, what = whatarg, multi.line = T)	#
#
#unlist the numeric data & convert to matrix, use first element
#of list (patient ids) as rownames
#
	mat.x <- matrix(unlist(list.x[2:57]), ncol = 56)
	dimnames(mat.x) <- list(list.x[[1]], c("C.1.5", "C.2.5", "C.3.5", 
		"C.4.5", "C.5.5", "C.6.5", "C.7.5", "C.8.5", "C.9.5", "C.10.5", 
		"C.11.5", "C.12.5", "BE1.1.5", "BE1.2.5", "BE1.3.5", "BE1.4.5", 
		"BE10.1.5", "BE10.2.5", "BE10.3.5", "BE10.4.5", "BE100.1.5", 
		"BE100.2.5", "BE100.3.5", "BE100.4.5", "C.1.7", "C.2.7", 
		"C.3.7", "C.4.7", "C.5.7", "C.6.7", "C.7.7", "C.8.7", "C.9.7", 
		"C.10.7", "C.11.7", "C.12.7", "BE1.1.7", "BE1.2.7", "BE1.3.7", 
		"BE1.4.7", "BE10.1.7", "BE10.2.7", "BE10.3.7", "BE10.4.7", 
		"BE100.1.7", "BE100.2.7", "BE100.3.7", "BE100.4.7", "PHA.1", 
		"PHA.2", "PHA.3", "PHA.4", "CAND.1", "CAND.2", "CAND.3", 
		"CAND.4"))	#
#
# now break apart bedata & nedata based on "AC" & "OR" values in row labels
#
	rowlabel.list <- dimnames(mat.x)[1]	# get row labels
	rowlabel.vec <- unlist(rowlabel.list)	# coerece to vector
	rowlabel.sub <- substring(rowlabel.vec, 1, 2)	# first 2 characters
#
# assign matrices
#
	assign("bedata", mat.x[rowlabel.sub == "AC",  ], w = 1)
	assign("nedata", mat.x[rowlabel.sub == "OR",  ], w = 1)

}
#