Description Usage Arguments Value Examples

View source: R/evaluateCorrDecay.R

For pairs of features evaluate the physical distance and the correlation

1 | ```
evaluateCorrDecay(treeList, gr, chromArray = seqlevels(gr), verbose = TRUE)
``` |

`treeList` |
list of hclust objects |

`gr` |
GenomicRanges object corresponding to features clustered in treeList |

`chromArray` |
Use this only this set of chromosmes. Can substantially reduce memory usage |

`verbose` |
show progress |

a data.frame of distance and correlation value for all pairs of features already evalauted in treeList. Note that runOrderedClusteringGenome() that returns treeList only evalutes correlation between a specified number of adjacent peaks

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
library(GenomicRanges)
library(ggplot2)
data('decorateData')
# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation )
# Evaluate how correlation between features decays with distance
dfDist = evaluateCorrDecay( treeList, simLocation )
# make plot
plotCorrDecay( dfDist )
``` |

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