Description Usage Arguments Author(s) Examples
Implementations of the outlying degree and Zscore methodologies desribed in Bottomly et al 2013.
1 2 3 4 5 6 7 8 | ## S4 method for signature 'ExpressionSet'
outlyingDegree(obj, k, type=c("non.weight", "weight.before", "weight.after"), weight.func=default.weight.func)
## S4 method for signature 'matrix'
outlyingDegree(obj, k, type=c("non.weight", "weight.before", "weight.after"), weight.func=default.weight.func)
## S4 method for signature 'ExpressionSet'
zScore(obj, robust=FALSE)
## S4 method for signature 'matrix'
zScore(obj, robust=FALSE)
|
obj |
Either a |
k |
An integer value that can range from 1 to ncol(obj)-1 |
type |
One of either "non.weight", "weight.before" or "weight.after" which corresponds to the standard outlying degree method, whether to apply the weights specified in |
weight.func |
A function returning a square matrix containing the weights corresponding to the sample-sample dissimilarities. |
robust |
Whether a robust Zscore should be computed e.g. (x-median(x))/mad(x) |
Daniel Bottomly
1 2 3 4 5 6 7 8 9 10 | data(simEset)
out.deg.eset <- outlyingDegree(simEset, k=1)
cur.mat <- exprs(simEset)
out.deg.mat <- outlyingDegree(cur.mat, k=1)
all.equal(out.deg.eset, out.deg.mat)
zscore.eset <- zScore(simEset)
zscore.mat <- zScore(cur.mat)
all.equal(zscore.eset, zscore.mat)
|
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