arrayQuality (version 1.50.0)

readSpikeTypes: Read Spike Types File

Description

Read a table containing information about the doping control mixture used in the hybridization.

Usage

readSpikeTypes(file = "DopingTypeFile2.txt", path = NULL, cy5col = "MassCy5", cy3col = "MassCy3", ...)

Arguments

file

A "character" string giving the name of the file specifying the doping controls used.

path

A "character" string giving the directory containing the file. By default this is set to the current working directory (".").

cy5col

A "character" string describing the name of the column corresponding to the controls labelled with Cy5.

cy3col

A "character" string describing the name of the column corresponding to the controls labelled with Cy3.

...

Additional arguments passed to "readSpotTypes"

Value

A list of n matrices, each matrix containing information about a unique type of spiked controls.

Details

The file is a text file with rows corresponding to doping controls and columns describing various experimental conditions. It must contain an oligo sequence identifier for each control, the spike type (e.g. Ambion or MJ) and the mass of each oligo spiked in each channel. By default, this function assumes that the mass unit are the same.

Examples

datadir <- system.file("Meebo", package="arrayQuality")
if (interactive())
{
spikes <-
readSpikeTypes(file="StanfordDCV1.7complete.txt",path=datadir,cy5col="CY5.ng._MjDC_V1.7",cy3col="CY3.ng._MjDC_V1.7")
}