clusterTSS: Cluster TSSs into tag clusters

In Linlab-slu/TSSr: TSS sequencing data analysis

Cluster TSSs into tag clusters

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

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.

Value

Large List of elements - one element for each sample

Examples

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

Linlab-slu/TSSr documentation built on Oct. 23, 2024, 8:31 p.m.