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. ... 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
`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 1.2.0 Index]