readDesign {HELP} | R Documentation |
Function to extract array design information from corresponding files in the Nimblegen .ndf and .ngd formats.
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, |
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, |
z |
object in which to store design information from files. Can be an |
... |
Arguments to be passed to methods (see
|
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")