loadPairFile: A routine to read Nimblegen tiling array intensities

In markrobinsonuzh/Repitools: Epigenomic tools

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)
#

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.