# Analysis of core promoter shape

`shapeCluster.Rd`

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).

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

    # S4 method for 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

    # \donttest{
            shapeCluster(exampleTSSr,clusters = "consensusClusters" , method = "PSS")#>
    #> Calculating consensusClusters shape with PSS method...        shapeCluster(exampleTSSr,clusters = "tagClusters" , method = "SI")#>
    #> Calculating tagClusters shape with SI method...# }