read.spike: Read SpikeList from a RGList\_CALIB and Concentration files

Description

Reads a SpikeList from a given RGList\_CALIB object and user specified concentration files

Usage

read.spike(RG, file = NULL, path = NULL, ext = NULL, sep = "\t", conccol, regexpcol, different = FALSE, ...)

Arguments

a RGList_CALIB object.

file

character string giving the name of the concentration file.

path

character string giving the directory containing the file. Can be omitted if the file is in the current working directory.

ext

character string giving optional extension to be added to each file name.

sep

field separator character.

conccol

list with fields RConc, GConc giving the column names to be used for red and green concentration in the concentration file.

regexpcol

character vector giving regular expressions in the concentration file.

different

a logical value. TRUE means that different arrays use different spikes. So every array should have one concentration file. FALSE means that different arrays use the same spike and only one concentration file is needed. Default is FALSE.

...

any other arguments are passed to read.table.

Value

R: matrix containing the red channel foreground intensities for each spot for each array.
G: matrix containing the green channel foreground intensities for each spot for each array.
Rb: matrix containing the red channel background intensities for each spike for each array.
Gb: matrix containing the green channel background intensities for each spike for each array.
RArea: matrix containing the red spot area for each spike for each array.
GArea: matrix containing the green spot area for each spike for each array.
RConc: matrix containing the red concentration for each spike for each array.
GConc: matrix containing the green concentration for each spike for each array.
genes: data frame containing annotation information about the probes, for example, spike types and IDs and spatial positions on the array

Details

This is the function to generate SpikeList in the CALIB package. SpikeList contains all the information for the spikes. This function exacts foreground and background intensities and spot area from RGList\_CALIB, which is generated from funtion read.rg. Also this funtion reads concentrations for each spike from a user-specified concentration file (or more than one concentration files if different arrays use different spikes).

For the concentration file, it should contain the following columns: regular expression, red and green concentrations and spike type. Spike type should be in the set of Calibration, Ratio and Negative.

See the CALIB User's Guide for the example of this function.

References

~put references to the literature/web site here ~