HELP (version 1.30.0)

readDesign: 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

\dots

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)

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")