SiteSetList {TFBSTools} | R Documentation |
"SiteSetList"
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.
## Constructors: SiteSetList(..., use.names=TRUE)
... |
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 |
A SiteSetList
object.
signature(x = "SiteSetList")
(x, type=c("TFMPvalue", "sampling")):
Calculates the empirical p-values for the scores.
Ge Tan
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")