quantifyClusters: Quantify expression of clusters (TSSs or enhancers) by...

Description Usage Arguments Value See Also Examples

View source: R/quantify.R

Description

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

Usage

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

Arguments

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.

Value

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

See Also

Other Quantification functions: quantifyCTSSs, quantifyGenes

Examples

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# 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)

MalteThodberg/CAGEfightR documentation built on Oct. 24, 2018, 12:10 p.m.