1 |
object |
|
Scale |
|
Cy |
|
Ref |
|
GC |
|
gcDB |
|
preSeg |
|
suppOutliers |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (object, Scale = TRUE, Cy = TRUE, Ref = "cy3", GC = TRUE,
gcDB = agilentDB, preSeg = TRUE, suppOutliers = FALSE)
{
cnSet <- getCNset(object)
if (grepl("Agilent", getInfo(object, "platform"))) {
if (Cy) {
cnSet <- .CyAdjust(cnSet, Ref)
object@param$CyAdjusted = TRUE
}
if (GC) {
cnSet <- .GCadjust(cnSet, gcDB)
object@param$GCAdjusted = TRUE
}
}
else {
object@param$CyAdjusted = FALSE
object@param$GCAdjusted = FALSE
}
object@param$dLRs <- .dlrs(cnSet$Log2Ratio)
object@param$MAD <- .MAD(cnSet$Log2Ratio)
if (Scale) {
cat("Scaling...")
cnSet$Log2Ratio <- scale(cnSet$Log2Ratio, center = FALSE)
if (grepl("Affymetrix", getInfo(object, "platform")))
cnSet$Log2Ratio <- cnSet$Log2Ratio * 1.25
cat("Done.\n")
}
if (suppOutliers)
cnSet$Log2Ratio <- .supprOutliers(cnSet$Log2Ratio, n = ifelse(grepl("Agilent",
getInfo(object, "platform")), 5, 25))
if (preSeg) {
cnSet <- .preSeg(cnSet, getInfo(object, "sampleName"),
getParam(object))
}
object@cnSet <- cnSet
cat("dLRs:", object@param$dLRs, "\tMAD:", object@param$MAD,
"\n")
return(object)
}
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