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).
# 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),]