loadPairFile {Repitools} | R Documentation

## A routine to read Nimblegen tiling array intensities

### Description

Reads a file in Nimblegen pair format, returning log2 intensities of probes referenced by the supplied ndf data frame.

### Usage

    loadPairFile(filename = NULL, ndf = NULL, ncols = 768)

### Arguments

`filename` | the name of the pair file which intensities are to be read from.
`ndf` | a data frame produced by `processNDF`.
`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 from the specified pair file, then matches probes against those specified in the supplied ndf.

### Value

a `vector` of log2 intensities, the number of rows of the supplied `ndf` in length.

### Author(s)

Aaron Statham

### See Also

`loadSampleDirectory` for reading multiple pair files with the same ndf. `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 pair file using the chromosome only NDF
    # arrayIntensity <- loadPairFile("Pairs/Array1_532.pair", ndf)
    #

[Package Repitools version 1.33.3 Index]