Repitools (version 1.18.0)

processNDF: 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.

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

Details

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

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),]