read.spike {CALIB} | R Documentation |
Reads a SpikeList from a given RGList_CALIB object and user specified concentration files
read.spike(RG, file = NULL, path = NULL, ext = NULL, sep = "\t", conccol, regexpcol, different = FALSE, ...)
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 . |
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.
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 |
Hui Zhao
~put references to the literature/web site here ~