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How to rewrite an old code with the new format #2

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arnaghizadeh opened this issue Aug 3, 2020 · 0 comments
Open

How to rewrite an old code with the new format #2

arnaghizadeh opened this issue Aug 3, 2020 · 0 comments

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@arnaghizadeh
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Hi, I have a code which seems to be compatible with an old version of ascend, here is the code, some functions are not found, may I know what version of the code this is compatible with and how I can transform it into the new format?

emset <- NewEMSet(ExpressionMatrix = dat)
normset <- NormaliseByRLE(emset)
pcaset <- RunPCA(normset)
pcaset <- ReduceDimensions(pcaset, n = params$nPC)
resset <- RunCORE(pcaset, conservative = TRUE, nres = 40, 
remove_outlier = TRUE)
ks <- resset@Clusters$KeyStats
ks <- subset(ks, ClusterCount == k)
height <- ks$Height[which.max(ks$RandIndex)]
cluster <- resset@Clusters$ClusteringMatrix[, height]
names(cluster) <- rownames(resset@Clusters$ClusteringMatrix)
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