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 1.0.0 Index]