PredicttransMEME: MAST algorithm to detect TFBS in a sequence
In MEET: MEET: Motif Elements Estimation Toolkit
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
View source: R/PredicttransMEME.R
Description
PWM in transfac format is used to find TFBS into a query sequence.
Usage
1
PredicttransMEME(iicc,TF)
Arguments
iicc
options of the MEET program
TF
Transcription Factor
Details
Uses the transMEME constructed motif
Value
output: the detected sequences and its position within the sequence.
Detected Factors
factors detected
P-value
Similarity Score
Position
Position of the detected BS within the large DNA sequence
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu>
See Also
MEET, kfold.transMEME, ModeltransMEME
Examples
1
2
3
4
5
6
data(iicc)
data(TranscriptionFactor)
iicc$method<-"transMEME"
pathMEET<-system.file("exdata",package="MEET")
#ModelTFBs<-ModeltransMEME(iicc)
#DetectedSequences<-PredicttransMEME(iicc, TF=paste(pathMEET,"AP1.fa",sep="/"))
MEET documentation built on May 2, 2019, 5:52 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/PredicttransMEME.R
Description
PWM in transfac format is used to find TFBS into a query sequence.
Usage
1 | PredicttransMEME(iicc,TF)
|
Arguments
iicc |
options of the MEET program |
TF |
Transcription Factor |
Details
Uses the transMEME constructed motif
Value
output: the detected sequences and its position within the sequence.
Detected Factors |
factors detected |
P-value |
Similarity Score |
Position |
Position of the detected BS within the large DNA sequence |
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu>
See Also
MEET, kfold.transMEME, ModeltransMEME
Examples
1 2 3 4 5 6 | data(iicc)
data(TranscriptionFactor)
iicc$method<-"transMEME"
pathMEET<-system.file("exdata",package="MEET")
#ModelTFBs<-ModeltransMEME(iicc)
#DetectedSequences<-PredicttransMEME(iicc, TF=paste(pathMEET,"AP1.fa",sep="/"))
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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