Rdocumentation
powered by
Learn R Programming
MEET (version 5.1.1)
MEET: Motif Elements Estimation Toolkit
Description
MEET (Motif Elements Estimation Toolkit) is a R-package that integrates a set of computational algorithms for the detection of Transcription Factor Binding Sites (TFBS).
Copy Link
Link to current version
Version
Version
5.1.1
Install
install.packages('MEET')
Monthly Downloads
19
Version
5.1.1
License
GPL (>= 2)
Maintainer
Joan Maynou
Last Published
February 22nd, 2013
Functions in MEET (5.1.1)
Search all functions
detector_1rOrdre_diff
Detection of Transcription Factor Binding Sites Through Differential Renyi Entropy
writeMEME
Write a training matrix in a MEME/MAST format
Prob
Probabilities of each nucleotide in the
Homo sapiens
organism according to Thakurta et al.
CalculSimilarity
Similarity Score between a Sequence and a PSSM model
readMEME
Read MEME motifs and consensus sequences
CalculPWM
CalculPWM: To calculate Position Weight Matrix
EntropyRATTUS
EntropyRATTUS: Given a Transcription factor chooses the model for a specific organism and method.
DivergenceMUS
DivergenceMUS: Given a Transcription factor chooses the model for a specific organism and method.
iicc
A set of initial conditions
standardout
Standard output detector
scoreMDscan
Output MDscan method
joint.probability
Joint Probability
CalculRedundancy
CalculRedundancy: To calculate the redundancy
Hmemory
Library of entropy values
ModelMATCH
Match algorithm to detect TFBS in a sequence
ModelDivergence
To create Model Divergence
MImemory
Library of PredictDivergence values
run.read.MDscan
Run and read MDscan on validation
PredictMATCH
MATCH algorithm to detect TFBS in a sequence
PredictMEME
MEME algorithm to detect TFBS in a sequence
EntropyMUS
EntropyMUS: Given a Transcription factor chooses the model for a specific organism and method.
PredictPCA
Q-residuals detection of TFBS, using a principal components model
TFlogodds
Logodds matrix
DivergenceDROSOPHILA
DivergenceDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method.
CalculInformation
Information content in each position of a set of aligned DNA sequences
Hread
To read Entropy values
QresidualsMUS
QresidualsMUS: Given a Transcription factor chooses the model for a specific organism and method.
ReadSequence
Convert a DNA sequence in a numerical DNA matrix
align.clustalw
Multiple sequence alignment by means of ClustalW
DivergenceRATTUS
DivergenceRATTUS: Given a Transcription factor chooses the model for a specific organism and method.
Models
To create Detection Model
align.muscle
Multiple sequence alignment by means of Muscle (MUltiple Sequence Comparison by Log-Expectation)
ModelPCA
PCA model for a set of TFBS
Read.aligned
Read nucleotide sequences
correction.entropy
Correction entropy from the Finite Sample Size Effect
entropy.Renyi
Renyi Entropy
kfold.PCA
PCA
Sequence
A sequence with binding evidence.
Model-class
A set of Models for the detection
kfold.MATCH
MATCH validation process
ModelEntropy
To create Model Entropy
probability.couple
Background joint probability
QtoJackson
Q to Jackson: transform a Q-residual into a confidence interval
divergence.Shannon
Divergencia.Shannon: Mutual Information
EntropyDROSOPHILA
EntropyDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method.
divergence.Renyi
Renyi divergence
detection
Detection: A set of functions for detection of TFBS
entropy.corrected
Correction of the Finite Sample Size Effect
JacksonParameters
JacksonParameters: To calculates the parameters needed to transform a Q-residual to a confidence interval
q
Renyi Order
ModeltransMEME
To create Model transMEME
classMODEL
classMODEL: To choose the model
numericalDNA
Conversion of nucleotides to numerical vectors
PredictMDscan
MDscan algorithm to detect TFBS in a sequence
EntropyHOMO
EntropyHOMO: Given a Transcription factor chooses the model for a specific organism and method.
ModelMDscan
MDscan algortihm to detect TFBS within a sequence
QresidualsRATTUS
QresidualsRATTUS: Given a Transcription factor chooses the model for a specific organism and method.
organism
Probability for each nucleotide according to different organism
BackgroundOrganism
Probabilities of each nucleotide in the
Homo sapiens
organism according to Thakurta et al.
detector_2nOrdre_init
Detection of Transcription Factor Binding Sites Through Parametric PredictDivergence
DivergenceHOMO
DivergenceHOMO: Given a Transcription factor chooses the model for a specific organism and method.
correctionaprox
Correction Entropy Approximate from the Finite Sample Size Effect.
PredictDivergence
A set of functions for detection of Transcription Factor Binding Sites by means of Divergence
diffInstructions
The measurement of the variation of the total redundancy
read.mast
Read output mast
ROCmodel
To choose the best paramater for a model
ModelMEME
MEME algortihm to detect TFBS within a sequence
correction.redundancy
Correction redundancy from the Finite Sample Size Effect
entropy.Shannon
Shannon Entropy
kfold.transMEME
Leave-one-out cross-validation for MEME/MAST through training.matrix aligned with MUSCLE or CLUSTALW.
motif.mast
MEME format to training matrix
align.MEME
Multiple sequence alignment by means of MEME.
PredicttransMEME
MAST algorithm to detect TFBS in a sequence
MIread
To read PredictDivergence values
probability
Probability
CreateConsensus
Consensus Sequence for a DNA motif
kfold.MEME
Leave-one-out cross-validation for MEME
correction-class
Correction for finite sample effect
CalculPSSM
Position Specific Scoring Matrices from a set of aligned sequences
PredictEntropy
PredictEntropy: Detection of Transcription Factor Binding Sites by means of Renyi entropy
kfold.MDscan
Leave-one-out cross-validation for MDscan.
CalculScores
Calcul Score of a Sequence, using a loggods matrix
redundancy
To calculate redundancy
QresidualsHOMO
QresidualsHOMO: Given a Transcription factor chooses the model for a specific organism and method.
PCanalysis
PC analysis on numerical DNA sequences
Prediction
To detect Transcription Factor Binding sites by means of a model
Alignment
To line up Transcription Factor Binding sites through Multiple Sequence Alignment (MSA)
ConstructModel
A set of functions for training of motif discovery algorithms.
kfold.Divergence
Leave-one-out cross-validation for parametric divergence (ITEME).
entropy.joint
To calculate joint entropy
QresidualsDROSOPHILA
QresidualsDROSOPHILA: Given a Transcription factor chooses the model for a specific organism and method.
detector_2nOrdre
Detection of Transcription Factor Binding Sites Through Parametric PredictDivergence
TranscriptionFactor
A set of aligned binding sites sequences
writeResultsHTML
Writes the results of a MEET detection to HTML.
MEET
MEET: Motif Elements Estimation Toolkit
pvalue
P value
kfold.Entropy
Leave-one-out cross-validation for Renyi entropy (ITEME)
chooseModel
ChooseModel: Choose the best model