### R code from vignette source 'LedPred.Rnw' ################################################### ### code chunk number 1: crm.features ################################################### library(LedPred) data(crm.features) ################################################### ### code chunk number 2: mapFeaturesToCRMs ################################################### dirPath <- system.file("extdata", package="LedPred") file.list <- list.files(dirPath, full.names=TRUE) background.freq <- file.list[grep("freq", file.list)] positive.regions <- file.list[grep("positive", file.list)] negative.regions <- file.list[grep("negative", file.list)] TF.matrices <- file.list[grep("tf", file.list)] ngs.path <- system.file("extdata/ngs", package="LedPred") ngs.files=list.files(ngs.path, full.names=TRUE) #crm.feature.list <- mapFeaturesToCRMs(URL = 'http://ifbprod.aitorgonzalezlab.org/map_features_to_crms.php', positive.bed=positive.regions, negative.bed=negative.regions, background.freqs=background.freq, pssm=TF.matrices, genome="dm3", ngs=ngs.files, crm.feature.file = "vignette_crm.features.tab", stderr.log.file = "vignette_stderr.log", stdout.log.file = "vignette_stdout.log") #names(crm.feature.list) #class(crm.feature.list$crm.features) ################################################### ### code chunk number 3: mcTune ################################################### #crm.features=crm.feature.list$crm.features #cost.vector <- c(1,3,10) #gamma.vector <- c(1,3,10) #c.g.obj <- mcTune(data = crm.features, ranges = list(cost=cost.vector, gamma=gamma.vector), kernel='linear', file.prefix = "vignette") #names(c.g.obj) #cost <- c.g.obj$e1071.tune.obj$best.parameters$cost #gamma <- c.g.obj$e1071.tune.obj$best.parameters$gamma ################################################### ### code chunk number 4: LedPred.Rnw:170-172 ################################################### #feature.ranking <- rankFeatures(data=crm.features, cost=cost, gamma=gamma, kernel='linear', file.prefix = "vignette") #head(feature.ranking) ################################################### ### code chunk number 5: LedPred.Rnw:178-181 ################################################### #feature.nb.tuner.obj <- tuneFeatureNb(data=crm.features, feature.ranking=feature.ranking, kernel='linear', cost=cost, gamma=gamma, file.prefix = "vignette") #names(feature.nb.tuner.obj) #feature.nb.tuner.obj$best.feature.nb ################################################### ### code chunk number 6: LedPred.Rnw:193-197 ################################################### #feature.nb <- 60 #model.obj <- createModel(data=crm.features, cost=cost, gamma=gamma, feature.ranking=feature.ranking, feature.nb=feature.nb, file.prefix="vignette") #names(model.obj) #model.obj$model ################################################### ### code chunk number 7: LedPred.Rnw:202-204 ################################################### #feature.weights <- as.data.frame(t(t(model.obj$model$coefs) %*% model.obj$model$SV)) #head(feature.weights) ################################################### ### code chunk number 8: LedPred.Rnw:210-211 ################################################### #probs.labels.list <- evaluateModelPerformance(data=crm.features, feature.ranking=feature.ranking, feature.nb=feature.nb, cost=cost, gamma=gamma, file.prefix = "vignette") ################################################### ### code chunk number 9: mapFeaturesToCRMs2 ################################################### dirPath <- system.file("extdata", package="LedPred") file.list <- list.files(dirPath, full.names=TRUE) background.freqs <- file.list[grep("freq", file.list)] positive.bed <- file.list[grep("prediction_small", file.list)] TF.matrices <- file.list[grep("259_matrices_lightNames", file.list)] ngs.path <- system.file("extdata/ngs", package="LedPred") ngs.files=list.files(ngs.path, full.names=TRUE) #prediction.crm.features.list <- mapFeaturesToCRMs(URL = 'http://ifbprod.aitorgonzalezlab.org/map_features_to_crms.php', positive.bed=positive.bed, # pssm=TF.matrices, background.freqs=background.freqs, # genome='dm3', ngs=ngs.files, feature.ranking=feature.ranking, feature.nb=feature.nb, # crm.feature.file = "vignette_pred.crm.features.tab", # stderr.log.file = "vignette_pred.stderr.log", stdout.log.file = "vignette_pred.stdout.log") #names(prediction.crm.features.list) #prediction.crm.features <- prediction.crm.features.list$crm.features ################################################### ### code chunk number 10: scoreData ################################################### #pred.test <- scoreData(data=prediction.crm.features, model=model.obj, score.file="vignette_prediction.tab") #pred.test ################################################### ### code chunk number 11: ledpred ################################################### crm.features=data(crm.features) cost.vector <- c(1,3,10) gamma.vector <- c(1,3,10) #ledpred.obj=LedPred(data=crm.features, cl=1, ranges = list(cost=cost.vector, gamma=gamma.vector), kernel="linear", file.prefix="vignette2") #names(ledpred.obj) ################################################### ### code chunk number 12: mapFeaturesToCRMs3 ################################################### dirPath <- system.file("extdata", package="LedPred") file.list <- list.files(dirPath, full.names=TRUE) background.freqs <- file.list[grep("freq", file.list)] positive.bed <- file.list[grep("prediction_small", file.list)] TF.matrices <- file.list[grep("259_matrices_lightNames", file.list)] ngs.path <- system.file("extdata/ngs", package="LedPred") ngs.files=list.files(ngs.path, full.names=TRUE) #prediction.crm.features.obj2 <- mapFeaturesToCRMs(URL = 'http://ifbprod.aitorgonzalezlab.org/map_features_to_crms.php', positive.bed=positive.bed, # pssm=TF.matrices, background.freqs=background.freqs, # genome='dm3', ngs=ngs.files, feature.ranking=ledpred.obj$feature.ranking, feature.nb=ledpred.obj$feature.nb, # crm.feature.file = "vignette2_pred.crm.features.tab", # stderr.log.file = "vignette2_pred.stderr.log", stdout.log.file = "vignette2_pred.stdout.log") #names(prediction.crm.features.obj2) #prediction.crm.features2 <- prediction.crm.features.obj2$crm.features ################################################### ### code chunk number 13: scoreData2 (eval = FALSE) ################################################### ## #pred.test2 <- scoreData(data=prediction.crm.features2, model=ledpred.list$model.obj, score.file="vignette2_prediction.tab") ## #pred.test2 ################################################### ### code chunk number 14: LedPred.Rnw:290-291 ################################################### sessionInfo()