Description Usage Arguments Value Methods Author(s) See Also Examples
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.
1 2 | ## 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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")
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