LedPred: Learning from DNA to Predict Enhancers

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This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.

Author
Elodie Darbo, Denis Seyres, Aitor Gonzalez
Date of publication
None
Maintainer
Aitor Gonzalez <aitor.gonzalez@univ-amu.fr>
License
MIT | file LICENSE
Version
1.8.0

View on Bioconductor

Man pages

createModel
Create the model with the optimal features
crm.features
This is data to be included in my package
evaluateModelPerformance
Evaluate model performances
feature.ranking
This is data to be included in my package
LedPred
Creates an SVM model given a feature matrix
mapFeaturesToCRMs
R interface to bed_to_matrix REST in server
mcTune
Tuning the SVM parameters
rankFeatures
Ranking the features according to their importance
scoreData
Predicting new regulatory regions
tuneFeatureNb
Selecting the optimal number of features

Files in this package

LedPred/DESCRIPTION
LedPred/LICENSE
LedPred/NAMESPACE
LedPred/NEWS
LedPred/R
LedPred/R/Data.R
LedPred/R/FeatureNbTuner.R
LedPred/R/FeatureRanking.R
LedPred/R/LedPredClass.R
LedPred/R/Model.R
LedPred/R/ModelPerformance.R
LedPred/R/ParameterTuner.R
LedPred/R/createModel.R
LedPred/R/evaluateModelPerformance.R
LedPred/R/ledpred.R
LedPred/R/mapFeaturesToCRMs.R
LedPred/R/mcTune.R
LedPred/R/rankFeatures.R
LedPred/R/scoreData.R
LedPred/R/tuneFeatureNb.R
LedPred/build
LedPred/build/vignette.rds
LedPred/data
LedPred/data/crm.features.rda
LedPred/data/feature.ranking.rda
LedPred/inst
LedPred/inst/CITATION
LedPred/inst/doc
LedPred/inst/doc/LedPred.R
LedPred/inst/doc/LedPred.Rnw
LedPred/inst/doc/LedPred.pdf
LedPred/inst/extdata
LedPred/inst/extdata/259_matrices_lightNames.tf
LedPred/inst/extdata/2nt_intergenic_droso.freq
LedPred/inst/extdata/negative_50CADenhancers.bed
LedPred/inst/extdata/ngs
LedPred/inst/extdata/ngs/K4me1_E_F_6_8h_H3_subtracted_reduced.wig
LedPred/inst/extdata/ngs/docBoundCRM.bed
LedPred/inst/extdata/ngs/dtcfBoundCRM.bed
LedPred/inst/extdata/ngs/pmadBoundCRM.bed
LedPred/inst/extdata/ngs/pnrBoundCRM.bed
LedPred/inst/extdata/ngs/tinBoundCRM.bed
LedPred/inst/extdata/positive_50CADenhancers.bed
LedPred/inst/extdata/prediction_small.bed
LedPred/inst/extdata/testdata
LedPred/inst/extdata/testdata/230NonActivesEnhancers4_8h_2seqs.bed
LedPred/inst/extdata/testdata/23From66ActiveEnhancersInMesoAt68h_2seqs.bed
LedPred/inst/extdata/testdata/feature_nb.txt
LedPred/inst/extdata/testdata/feature_rank.txt
LedPred/inst/extdata/testdata/test_ngs_bed_small
LedPred/inst/extdata/testdata/test_ngs_bed_small/mfile2.tf
LedPred/inst/extdata/testdata/test_ngs_bed_small/negative_5seqs.bed
LedPred/inst/extdata/testdata/test_ngs_bed_small/ngs_beds
LedPred/inst/extdata/testdata/test_ngs_bed_small/ngs_beds/ngs.bed
LedPred/inst/extdata/testdata/test_ngs_bed_small/ngs_beds/ngs2.bed
LedPred/inst/extdata/testdata/test_ngs_bed_small/outdir_bak
LedPred/inst/extdata/testdata/test_ngs_bed_small/outdir_bak/feature_matrix.tab
LedPred/inst/extdata/testdata/test_ngs_bed_small/positive_2seqs.bed
LedPred/man
LedPred/man/LedPred.Rd
LedPred/man/createModel.Rd
LedPred/man/crm.features.Rd
LedPred/man/evaluateModelPerformance.Rd
LedPred/man/feature.ranking.Rd
LedPred/man/mapFeaturesToCRMs.Rd
LedPred/man/mcTune.Rd
LedPred/man/rankFeatures.Rd
LedPred/man/scoreData.Rd
LedPred/man/tuneFeatureNb.Rd
LedPred/tests
LedPred/tests/testthat
LedPred/tests/testthat.R
LedPred/tests/testthat/_ROC_perf.png
LedPred/tests/testthat/_kappa_measures.png
LedPred/tests/testthat/data_iris2
LedPred/tests/testthat/data_iris2/feature.ranking.rda
LedPred/tests/testthat/data_iris2/iris2.rda
LedPred/tests/testthat/data_iris2/x.rda
LedPred/tests/testthat/data_iris2/y.rda
LedPred/tests/testthat/test-iris2_Data.R
LedPred/tests/testthat/test-iris2_FeatureNbTuner.R
LedPred/tests/testthat/test-iris2_FeatureRanking.R
LedPred/tests/testthat/test-iris2_LedPred.R
LedPred/tests/testthat/test-iris2_ModelCreate.R
LedPred/tests/testthat/test-iris2_ModelPerformance.R
LedPred/tests/testthat/test-iris2_ParameterTuner.R
LedPred/vignettes
LedPred/vignettes/LedPred.Rnw
LedPred/vignettes/_ROCR_perf.png
LedPred/vignettes/_c_g_eval.png
LedPred/vignettes/_kappa_measures.png
LedPred/vignettes/figs
LedPred/vignettes/figs/vignette_ROC_perf.png
LedPred/vignettes/figs/vignette_c_g_eval.png
LedPred/vignettes/figs/vignette_kappa_measures.png