R: transformations of expression data in smlSet instances
clipPCs
R Documentation
transformations of expression data in smlSet instances
Description
transformations of expression data in smlSet instances
or assay data in SummarizedExperiment
Usage
clipPCs(x, inds2drop, center = TRUE)
regressOut(sms, rhs, ...)
Arguments
x
instance of smlSet
or RangedSummarizedExperiment
sms
instance of smlSet
or RangedSummarizedExperiment
inds2drop
Vector of PCs to be eliminated by setting the associated diagonal elements in the
SVD to zero before recomposing the matrix of expression values. If the value 0
is present in inds2drop, the smlSet is returned unchanged, with a message.
center
logical, passed to prcomp
rhs
formula fragment (no dependent variable) used to form residuals
in a reexpression of the expression matrix; variable bindings
found in pData of an ExpressionSet or colData of a SummarizedExperiment
...
arguments passed to lmFit
Details
clipPCs is an operation on the n x p transposed matrix X of expression data.
The singular value decomposition X = UDV^t is formed, the diagonal elements of D
corresponding to inds2drop are set to zero yielding the diagonal matrix E, and
then Y = UEV^t is computed and transposed to replace the expression data.
regressOut obtains residuals after genewise regression of expression on
the design matrix specified by the rhs; lmFit is used to
compute coefficients, linear predictions and residuals.
Value
an instance of smlSet
Author(s)
VJ Carey <stvjc@channing.harvard.edu>
References
The use of PCA-based adjustments to remove mass extraneous effects from
expression matrices has been criticized in work of Oliver Stegle and Jeffrey Leek,
who offer Bayesian PEER and SVA respectively as alternative solutions.
The PCA-based method seems to have reasonable
effectiveness in examples worked with GGdata.
Examples
## Not run: # this would induce cyclic dependency, but should
# run manually
if ("GGtools" %in% installed.packages()[,1]) {
require("GGtools")
c20 = getSS("GGtools", "20")
t1 = gwSnpTests(genesym("CPNE1")~male, c20, chrnum("20"))
topSnps(t1)
c20c = clipPCs(c20, 1:10)
t2 = gwSnpTests(genesym("CPNE1")~male, c20c, chrnum("20"))
topSnps(t2)
}
## End(Not run)