loadPairFile: A routine to read Nimblegen tiling array intensities
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

Reads in intensities from the specified pair file, then matches probes against those specified in the supplied ndf.

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

Aaron Statham

loadSampleDirectory for reading multiple pair files with the same ndf. processNDF

# 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)
#