shapeCluster: Analysis of core promoter shape

In Linlab-slu/TSSr: TSS sequencing data analysis

Analysis of core promoter shape

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

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.

Value

Large List of elements - one element for each sample

Examples

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

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