processNDF {Repitools} | R Documentation

## Reads in a Nimblegen microarray design file (NDF)

### Description

Reads a Nimblegen microarray design file (NDF file) which describes positions and sequences of probes on a Nimblegen microarray.

### Usage

    processNDF(filename = NULL, ncols = 768)

### Arguments

`filename` | the name of the Nimblegen microarray design file
`ncols` | the number of columns of probes on the array - must be the same value as will be passed to `loadPairFile` or `loadSampleDirectory`. The default works for 385K format arrays.

### Details

Reads in a Nimblegen microarray design file. This enables the reading in and annotation of Nimblegen microarray data files (pair files).

### Value

a data frame containing

`chr` | the chromosome the probe was designed against
`position` | the position of the sequence the probe was designed against (probe centre)
`strand` | the strand the probe was designed against
`index` | the index (x y position) the probe occupies on the array
`sequence` | the actual DNA sequence synthesised onto the array
`GC` | the percent GC content of the probe sequence

### Author(s)

Aaron Statham

### See Also

`loadSampleDirectory`, `loadPairFile`

### 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),]

[Package Repitools version 1.38.0 Index]