SiteSetList-class: Class '"SiteSetList"'

In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

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")

ge11232002/TFBSTools documentation built on Sept. 12, 2021, 12:07 p.m.