Nothing
library("aroma.affymetrix")
verbose <- Verbose(threshold=-4, timestamp=TRUE)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# doCBS() with explicit data set tuple
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "HapMap,CEU,testset"
tags <- "ACC,-XY,RMA,+300,A+B,FLN,-XY"
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
nbrOfSets <- length(chipTypes)
dsList <- vector("list", nbrOfSets)
for (kk in seq_len(nbrOfSets)) {
chipType <- chipTypes[kk]
ds <- CnChipEffectSet$byName(dataSet, tags=tags, chipType=chipType,
mergeStrands=TRUE, combineAlleles=TRUE)
dsList[[kk]] <- ds
}
print(dsList)
dsTuple <- as.CopyNumberDataSetTuple(dsList)
print(dsTuple)
res <- doCBS(dsTuple, arrays=1:2, chromosomes=c(19,21), verbose=verbose)
print(res)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# doCBS() with data set tuple names
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "HapMap270,100K,CEU,testSet"
tags <- "ACC,-XY,RMA,+300,A+B,FLN,-XY"
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
res <- doCBS(dataSet, tags=tags, chipTypes=chipTypes,
arrays=1:2, chromosomes=c(19,21), verbose=verbose)
print(res)
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