shapeCluster: Analysis of core promoter shape

Description Usage Arguments Examples

Description

Calculates core promoter shape based on the distributions of TSSs within core promoters using Shape Index (SI) algorithm (Hoskins et al. 2011) or Promoter Shape Score (PSS) algorithm (Lu et al. 2019).

Usage

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shapeCluster(object, clusters = "consensusClusters", method = "PSS",
 useMultiCore=FALSE, numCores = NULL)

## S4 method for signature 'TSSr'
shapeCluster(
  object,
  clusters = "consensusClusters",
  method = "PSS",
  useMultiCore = FALSE,
  numCores = NULL
)

Arguments

object

A TSSr object.

clusters

Clusters to be used for calculating shape score: "tagClusters" or "consensusClusters". Default is "consensusClusters".

method

Method to be used for calculating core promoter shape score: "SI" or "PSS". Default is "PSS".

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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	shapeCluster(exampleTSSr,clusters = "consensusClusters" , method = "PSS")
	shapeCluster(exampleTSSr,clusters = "tagClusters" , method = "SI")

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