readDesign {HELP} | R Documentation

## Read NimbleGen design files

### Description

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

### Usage

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

### Arguments

`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` `...` other arguments to be passed to `read.table`. See `read.table`.

### Value

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)

### Author(s)

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

### See Also

`readDesign-methods`, `read.table`

### Examples

    #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")

[Package HELP version 1.0.0 Index]