findStretches: Find stretches of clusters

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

Description

Finds stretches or groups of clusters along the genome, where each cluster is within a certain distance of the next. Once stretches have been identified, the average pairwise correlation between all clusters in the stretch is calculated. A typical use case is to look for stretches of enhancers, often refered to as "super enhancers".

Usage

findStretches(object, ...)

## S4 method for signature 'GRanges'
findStretches(object, mergeDist = 10000L, minSize = 3L)

## S4 method for signature 'RangedSummarizedExperiment'
findStretches(
  object,
  inputAssay,
  mergeDist = 10000L,
  minSize = 3L,
  corFun = cor,
  ...
)

Arguments

object	GRanges or RangedSummarizedExperiment: Clusters, possibly with expression for calculating correlations.
...	additional arguments passed to methods or ultimately corFun.
mergeDist	integer: Maximum distance between clusters to be merged into stretches.
minSize	integer: Minimum number of clusters in stretches.
inputAssay	character: Name of assay holding expression values (if object is a RangedSummarizedExperiment)
corFun	function: Function for calculating correlations. Should behave and produce output similar to cor().

Value

A GRanges containing stretches with number of clusters and average pairwise correlations calculated. The revmap can be used to retrieve the original clusters (see example below.)

See Also

Other Spatial functions: findLinks(), trackLinks()

Examples

# Calculate TPM values for bidirectional clusters
data(exampleBidirectional)
BCs <- calcTPM(exampleBidirectional)

# Find stretches
pearson_stretches <- findStretches(BCs, inputAssay="TPM")

# Use Kendall instead of pearson and require bigger stretches
kendall_stretches <- findStretches(BCs, inputAssay="TPM",
                                   minSize=5, method="kendall")

# Use the revmap to get stretches as a GRangesList
grl <- extractList(rowRanges(BCs), kendall_stretches$revmap)
names(grl) <- names(kendall_stretches)

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.