readPairs {HELP} | R Documentation |
Function to extract data from corresponding files in the Nimblegen .pair format.
readPairs(x, y, z, ...)
x |
the name of the file containing data from signal channel 1. Each line of the file is interpreted as a single data point. 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).
x can also be a complete URL. |
y |
the name of the file containing data from signal channel 1. Each line of the file is interpreted as a single data point. 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).
y can also be a complete URL. |
z |
object in which to store pair information from files. Can be an ExpressionSet , in which case pair data will be stored in featureData . |
... |
Arguments to be passed to methods (see readPairs-methods ):
name x .element.x AssayData (default is "exprs") in which to store signal channel 1 data.element.y AssayData (default is "exprs2") in which to store signal channel 2 data.match.probes featureData .path x and y ) are treated as is. comment.char sep quote quote = "" . See scan for the behaviour 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 pair information in assayData verbose ... read.table . See read.table . |
Returns an ExpressionSet
filled with assayData
containing matrices of data from both signal channels.
and featureData
containing the following featureColumns
:
|
a vector of characters with container IDs, linking each probe to a parent identifier |
|
a vector of characters containing unique ID information for each probe |
|
a vector of characters with .pair file locations for signal channel 1 data |
|
a vector of characters with .pair file locations for signal channel 2 data |
Reid F. Thompson (rthompso@aecom.yu.edu)
#demo(pipeline,package="HELP") x <- 1:500 y <- rev(x) data <- sample(8000:10000/1000,size=500) seqids <- sample(1:50,size=500,replace=TRUE) cat("#COMMENT\nSEQ_ID\tPROBE_ID\tX\tY\tPM\n",file="./read.pair.test.1") table.1 <- cbind(seqids,y,x,x,data) write.table(table.1,file="./read.pair.test.1",append=TRUE,col.names=FALSE,row.names=FALSE,quote=FALSE,sep="\t") cat("#COMMENT\nSEQ_ID\tPROBE_ID\tX\tY\tPM\n",file="./read.pair.test.2") table.2 <- cbind(seqids,y,x,x,rev(data)) write.table(table.2,file="./read.pair.test.2",append=TRUE,col.names=FALSE,row.names=FALSE,quote=FALSE,sep="\t") x <- readPairs("./read.pair.test.1","./read.pair.test.2") c(seqids[1],y[1],data[1],rev(data)[1]) pData(featureData(x))$"SEQ_ID"[1] pData(featureData(x))$"PROBE_ID"[1] assayDataElement(x, "exprs")[1] assayDataElement(x, "exprs2")[1] #rm(table.1,table.2,x,y,data,seqids) #file.remove("./read.pair.test.1") #file.remove("./read.pair.test.2")