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

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

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

Usage

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: quantifyCTSSs2(), quantifyCTSSs(), quantifyGenes()

Examples

# 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 Sept. 11, 2021, 4:42 a.m.