loadSampleDirectory {Repitools} | R Documentation

## A routine to read Nimblegen tiling array intensities

### Description

Reads all files in Nimblegen pair format within the specified directory, returning log2 intensities of probes referenced by the supplied ndf data frame.

### Usage

    loadSampleDirectory(path = NULL, ndf = NULL, what="Cy3", ncols = 768)

### Arguments

`path` | the directory containing the pair files to be read.
`ndf` | a data frame produced by `processNDF`.
`what` | specifies the channel(s) to be read in - either `Cy3`, `Cy5`, `Cy3/Cy5`, `Cy5/Cy3`, `Cy3andCy5`, `Cy5andCy3`.
`ncols` | the number of columns of probes on the array - must be the same value as used in `processNDF`. The default works for 385K format arrays.

### Details

Reads in intensities of all arrays contained within `path`. The parameter `what` determines which fluorescent channels are read, and how the are returned. `Cy3` and `Cy5` return the log2 intensity of the specified single channel. `Cy3/Cy5` and `Cy5/Cy3` return the log2 ratio of the two channels. `Cy3andCy5` and `Cy5andCy3` return the log2 intensity of both channels in separate columns of the matrix.

### Value

a `matrix` of log2 intensites, with the same number of rows as the supplied `ndf` and depending on the value of `what` either one or two columns per array.

### Author(s)

Aaron Statham

### See Also

`loadPairFile` for reading a single pair files. `processNDF`

### Examples

    # Not run
    #
    ## Read in the NDF file
    # ndfAll <- processNDF("080310_HG18_chr7RSFS_AS_ChIP.ndf")
    #
    ## Subset the NDF to only probes against chromosomes
    # ndf <- ndfAll[grep("^chr", ndfAll$chr),]
    #
    ## Read in a directory of pair files, returning both the Cy3 and Cy5 fluorescence in separate columns
    # arrayIntensities <- loadSampleDirectory("Arrays", ndf, what="Cy3andCy5")
    #

[Package Repitools version 1.30.0 Index]