loadSampleDirectory: A routine to read Nimblegen tiling array intensities

Description

Reads all files in Nimblegen pair format within the specified directory, returning log2 intensities of probes referenced by the supplied ndf data frame.

Usage

loadSampleDirectory(path = NULL, ndf = NULL, what="Cy3", ncols = 768)

Arguments

path

the directory containing the pair files to be read.

ndf

a data frame produced by processNDF.

what

specifies the channel(s) to be read in - either Cy3, Cy5, Cy3/Cy5, Cy5/Cy3, Cy3andCy5, Cy5andCy3.

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.

Value

a matrix of log2 intensites, with the same number of rows as the supplied ndf and depending on the value of what either one or two columns per array.

Details

Reads in intensities of all arrays contained within path. The parameter what determines which fluorescent channels are read, and how the are returned. Cy3 and Cy5 return the log2 intensity of the specified single channel. Cy3/Cy5 and Cy5/Cy3 return the log2 ratio of the two channels. Cy3andCy5 and Cy5andCy3 return the log2 intensity of both channels in separate columns of the matrix.

Examples

Run this code

# 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 directory of pair files, returning both the Cy3 and Cy5 fluorescence in separate columns
# arrayIntensities <- loadSampleDirectory("Arrays", ndf, what="Cy3andCy5")
#