readDesign: Read NimbleGen design files
In HELP: Tools for HELP data analysis

Description Usage Arguments Value Author(s) See Also Examples

Function to extract array design information from corresponding files in the Nimblegen .ndf and .ngd formats.

1	readDesign(x, y, z, ...)

`x`	path to the Nimblegen design file (.ndf). Each line of the file is interpreted as a single spot on the array design. If it does not contain an absolute path, the file name is relative to the current working directory, `getwd()`. Tilde-expansion is performed where supported. Alternatively, `x` can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). file can also be a complete URL.
`y`	path to the Nimblegen gene descriptions file (.ngd). Each line of the file is interpreted as a single locus. If it does not contain an absolute path, the file name is relative to the current working directory, `getwd()`. Tilde-expansion is performed where supported. Alternatively, `y` can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). file can also be a complete URL.
`z`	object in which to store design information from files. Can be an `ExpressionSet`, in which case design information will be stored in `featureData`.
`...`	Arguments to be passed to methods (see `readDesign-methods`): path a character vector containing a single full path name to which filenames will be appended. If NULL, filenames (`x` and `y`) are treated as is. comment.char character: a character vector of length one containing a single character or an empty string (default is "\#"). Use "" to turn off the interpretation of comments altogether. sep the field separator character (default is "\t"). Values on each line of the file are separated by this character. If sep = "" the separator is "white space", that is one or more spaces, tabs, newlines or carriage returns. quote the set of quoting characters (default is "\""). To disable quoting altogether, use `quote = ""`. See `scan` for the behavior on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless colClasses is specified. eSet `ExpressionSet` input (default is `new("ExpressionSet")`) in which to store design information in `featureData` \dots other arguments to be passed to `read.table`. See `read.table`.

Returns an ExpressionSet filled with featureData containing the following featureColumns:

`SEQ_ID`	a vector of characters with container IDs, linking each probe to a parent identifier
`PROBE_ID`	a vector of characters containing unique ID information for each probe
`X`	vector of numerical data determining x-coordinates of probe location on chip
`Y`	vector of numerical data determining y-coordinates of probe location on chip
`TYPE`	a vector of characters defining the type of probe, e.g. random background signals ("RAND") or usable data ("DATA").
`CHR`	a matrix of characters containing unique ID and chromosomal positions for each container
`START`	a matrix of characters containing unique ID and chromosomal positions for each container
`STOP`	a matrix of characters containing unique ID and chromosomal positions for each container
`SIZE`	a matrix of characters containing unique ID and chromosomal positions for each container
`SEQUENCE`	a vector of characters containing sequence information for each probe
`WELL`	a vector of characters containing multiplex well location for each probe (if present in design files)

Reid F. Thompson (rthompso@aecom.yu.edu)

readDesign-methods, read.table

#demo(pipeline, package="HELP")

chr <- rep("chr1", 500)
start <- (1:500)*200
stop <- start+199
x <- 1:500
seqids <- sample(1:50, size=500, replace=TRUE)
cat("#COMMENT\nSEQ_ID\tCHROMOSOME\tSTART\tSTOP\n", file="./read.design.test.ngd")
table.ngd <- cbind(seqids, chr, start, stop)
write.table(table.ngd, file="./read.design.test.ngd", append=TRUE, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
cat("#COMMENT\nSEQ_ID\tX\tY\tPROBE_ID\tCONTAINER\tPROBE_SEQUENCE\tPROBE_DESIGN_ID\n", file="./read.design.test.ndf")
sequence <- rep("NNNNNNNN", 500)
table.ndf <- cbind(seqids, x, x, x, x, sequence, x)
write.table(table.ndf, file="./read.design.test.ndf", append=TRUE, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
x <- readDesign("./read.design.test.ndf", "./read.design.test.ngd")
seqids[1:10]
pData(featureData(x))$"SEQ_ID"[1:10]

#rm(table.ngd, table.ndf, chr, start, stop, x, seqids, sequence)
#file.remove("./read.design.test.ngd")
#file.remove("./read.design.test.ndf")