clusterTSS: Cluster TSSs into tag clusters

Description Usage Arguments Examples

Description

Clusters TSSs within small genomic regions into tag clusters (TCs) using "peakclu" method. "peakclu" method is an implementation of peak-based clustering. The minimum distance of two neighboring peaks can be specified.

Usage

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clusterTSS(object, method = "peakclu", peakDistance=100,extensionDistance=30
, localThreshold = 0.02,clusterThreshold = 1, useMultiCore=FALSE, numCores=NULL)

## S4 method for signature 'TSSr'
clusterTSS(
  object,
  method = "peakclu",
  peakDistance = 100,
  extensionDistance = 30,
  localThreshold = 0.02,
  clusterThreshold = 1,
  useMultiCore = FALSE,
  numCores = NULL
)

Arguments

object

A TSSr object

method

Clustering method to be used for clustering: "peakclu". Default is "peakclu".

peakDistance

Minimum distance of two neighboring peaks. Default value = 100.

extensionDistance

Maximal distance between peak and its neighboring TSS or two neighboring TSSs to be grouped in the same cluster. Default value = 30.

localThreshold

Ignore downstream TSSs with signal < localThreshold*peak within clusters, which is used to filter TSS signals brought from possible recapping events, or sequencing noise. Default value = 0.02.

clusterThreshold

Ignore clusters if signal < clusterThreshold. Default value = 1.

useMultiCore

Logical indicating whether multiple cores are used (TRUE) or not (FALSE). Default is FALSE.

numCores

Number of cores are used in clustering step. Used only if useMultiCore = TRUE. Default is NULL.

Examples

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clusterTSS(exampleTSSr, method = "peakclu",clusterThreshold = 1, useMultiCore=TRUE, numCores = NULL)

Linlab-slu/TSSr documentation built on July 28, 2021, 12:59 a.m.