Description Usage Arguments Value See Also Examples

Quantify expression of clusters (TSSs or enhancers) by summing CTSSs within clusters.

1 | ```
quantifyClusters(object, clusters, inputAssay = "counts", sparse = FALSE)
``` |

`object` |
RangedSummarizedExperiment: CTSSs. |

`clusters` |
GRanges: Clusters to be quantified. |

`inputAssay` |
character: Name of assay holding expression values to be quantified (usually counts). |

`sparse` |
logical: If the input is a sparse matrix, TRUE will keep the output matrix sparse while FALSE will coerce it into a normal matrix. |

RangedSummarizedExperiment with row corresponding to clusters. seqinfo and colData is copied over from object.

Other Quantification functions:
`quantifyCTSSs2()`

,
`quantifyCTSSs()`

,
`quantifyGenes()`

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
# CTSSs stored in a RangedSummarizedExperiment:
data(exampleCTSS)
# Clusters to be quantified as a GRanges:
data(exampleUnidirectional)
clusters <- rowRanges(exampleUnidirectional)
# Quantify clusters:
quantifyClusters(exampleCTSSs, clusters)
# For exceptionally large datasets,
# the resulting count matrix can be left sparse:
quantifyClusters(exampleCTSSs, rowRanges(exampleUnidirectional), sparse=TRUE)
``` |

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