SiteSetList {TFBSTools} | R Documentation

## Class `"SiteSetList"`

### Description

The SiteSetList class is a container for storing a collection of SiteSet objects. Basically it is a SimpleList and is designed for manipulating the set of SiteSet objects as a whole.

### Usage

    ## Constructors:
      SiteSetList(..., use.names=TRUE)

### Arguments

`...` | The SiteSet objects are supplied in .... A list of SiteSet objects is also acceptable.
`use.names` | A logical value. When TRUE, the names of the `SiteSet` will be kept.

### Value

A `SiteSetList` object.

### Methods

pvalues

  `signature(x = "SiteSetList")` (x, type=c("TFMPvalue", "sampling")): Calculates the empirical p-values for the scores.

### Author(s)

Ge Tan

### See Also

`SiteSet`, `searchSeq`, `searchAln`

### Examples

      data(MA0003.2)
      data(MA0004.1)
      pwmList <- PWMatrixList(MA0003.2=toPWM(MA0003.2), MA0004.1=toPWM(MA0004.1))
      sitesetList <- searchSeq(pwmList, "GAATTCTCTCTTGTTGTAGTCTCTTGACAAAATG",
                               min.score="50%")

      ## elementNROWS of each pwm hits
      library(S4Vectors)
      elementNROWS(sitesetList)

      ## Output of SiteSetList
      writeGFF3(sitesetList, scoreType="absolute")
      as(sitesetList, "DataFrame")
      as(sitesetList, "data.frame")
      as.data.frame(sitesetList)
      as(sitesetList, "GRanges")

      ## Calculate the p-values
      pvalues(sitesetList, type="TFMPvalue")
      pvalues(sitesetList, type="sampling")

[Package TFBSTools version 1.18.0 Index]