# MEET: Motif Elements Estimation Toolkit

## Documentation for package ‘MEET’ version 5.1.1

- DESCRIPTION file.

## Help Pages

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