View source: R/local_correlations.R

scoreClusters | R Documentation |

For each cluster compute summary statistics for the cluster to measure how strong the correlation structure is. Clusters with weak correlation structure can be dropped from downstream analysis.

```
scoreClusters(treeList, treeListClusters, BPPARAM = SerialParam())
```

`treeList` |
list of hclust objects |

`treeListClusters` |
from createClusters() |

`BPPARAM` |
parameters for parallel evaluation |

For each cluster, extract the correlation matrix and return the mean absolute correlation; the 75th, 90th and 95th quantile absolute correlation, and LEF, the leading eigen-value fraction which is the fraction of variance explained by the leading eigen value of the matrix abs(C).

for all pairs of peaks within windowSize, report distance

```
library(GenomicRanges)
library(BiocParallel)
data('decorateData')
# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation )
# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList )
# Evaluate score for each cluster
clstScore = scoreClusters(treeList, treeListClusters, BPPARAM = SerialParam() )
```

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