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 ):
|
Returns an ExpressionSet
filled with assayData
containing matrices of data from both signal channels.
and 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 |
CHIPS |
a vector of characters with .pair file locations for signal channel 1 data |
CHIPS2 |
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")