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

In CALIB: Calibration model for estimating absolute expression levels from microarray data

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

RG	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.

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.

Value

An SpikeList object containing the components

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

Author(s)

Hui Zhao

References

~put references to the literature/web site here ~

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.