readPairs {HELP} | R Documentation |
Read Nimblegen .pair files
Description
Function to extract data from corresponding files in the Nimblegen .pair format.
Usage
readPairs(x, y, z, ...)
Arguments
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
character input specifying a sample name to assign to the data from specified pair files. If NULL (default), a value will be extracted from the filename specified in x .
- element.x
which element of AssayData (default is "exprs") in which to store signal channel 1 data.
- element.y
which element of AssayData (default is "exprs2") in which to store signal channel 2 data.
- match.probes
logical specifying whether to match data from pair files by "PROBE\_ID" with any pre-existing data. if TRUE (default), order of values will be rearranged so long as there are already "PROBE\_ID"s specified in featureData .
- 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 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
logical; if TRUE (default) progress will be output to screen. If FALSE, no output will be displayed.
- \dots
other arguments to be passed to read.table . See read.table .
|
Value
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
|
and phenoData
containing the following sampleColumns
:
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
|
Author(s)
Reid F. Thompson (rthompso@aecom.yu.edu)
See Also
readPairs-methods
, read.table
Examples
#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")
[Package
HELP version 1.44.0
Index]