character string. indicating the phenotype variable Hybridization_Name.
arrayType
A character string indicating if the correlations
are calculated based on all arrays, arrays with replicates,
or genetic control arrays.
GCid
A vector of character string. symbols for genetic control samples. The symbols
can be more than one.
probs
A vector of probabilities specify the quantiles of correlations
to be output.
col
colors used for the image. see the function heatmap.2
in R package gplots.
labelVariable
A character string indicating how to label the arrays.
outFileName
A character string.
The name of output file.
title
Title of the plot.
requireLog2
logical. requiredLog2=TRUE indicates probe expression levels
will be log2 transformed. Otherwise, no transformation will be performed.
plotOutPutFlag
logical. plotOutPutFlag=TRUE indicates the plots will be output
to pdf format files. Otherwise, the plots will not be output
to external files.
las
'las' numeric in 0,1,2,3; the style of axis labels.
0 - always parallel to the axis,
1 - always horizontal,
2 - always perpendicular to the axis,
or 3 - always vertical.
see par.
keysize
numeric value indicating the size of the key.
see the function heatmap.2
in R package gplots.
margins
numeric vector of length 2 containing the margins.
see the function heatmap.2
in R package gplots.
sortFlag
logical. Indicates if arrays need to be sorted according to
Batch_Run_Date, Chip_Barcode, and Chip_Address.
varSort
A vector of phenotype variable names to be used to sort the samples
of es.
timeFormat
A vector of time format for the possible time variables in varSort.
The length of timeFormat should be the same as that
of varSort. For non-time variable, the corresponding time format
should be set to be equal to NA. The details of the time format
for time variable can be found in the R function strptime.
...
Arguments to be passed to heatmap.2.
Value
A list with 3 elments. The first element R2Mat is
the matrix of squared correlation.
The second element R2vec is the vector of
the upper triangle of the matrix
of squared correlation (diagnoal elements are excluded).
The third element R2vec.within.req is the vector of
within-replicate R^2,
that is, any element in R2vec.within.req is the squared correlation
coefficient between two arrays/replicates for a subject.
Author(s)
Weiliang Qiu <stwxq@channing.harvard.edu>,
Brandon Guo <brandowonder@gmail.com>,
Christopher Anderson <christopheranderson84@gmail.com>,
Barbara Klanderman <BKLANDERMAN@partners.org>,
Vincent Carey <stvjc@channing.harvard.edu>,
Benjamin Raby <rebar@channing.harvard.edu>
providing 
.