## ----eval=TRUE---------------------------------------------------------------- library(DNAshapeR) ## ----eval=TRUE---------------------------------------------------------------- library(DNAshapeR) fn <- system.file("extdata", "CGRsample.fa", package = "DNAshapeR") pred <- getShape(fn) ## ----eval=FALSE--------------------------------------------------------------- # # Install Bioconductor packages # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("BSgenome.Scerevisiae.UCSC.sacCer3") # # library(BSgenome.Scerevisiae.UCSC.sacCer3) # # # Create a query GRanges object # gr <- GRanges(seqnames = c("chrI"), # strand = c("+", "-", "+"), # ranges = IRanges(start = c(100, 200, 300), width = 100)) # getFasta(gr, Scerevisiae, width = 100, filename = "tmp.fa") # fn <- "tmp.fa" # pred <- getShape(fn) ## ----eval=FALSE--------------------------------------------------------------- # # Install Bioconductor packages # library(BSgenome.Hsapiens.UCSC.hg19) # library(AnnotationHub) # # ah <- AnnotationHub() # ah <- subset(ah, species=="Homo sapiens") # ah <- query(ah, c("H3K4me3", "Gm12878", "Roadmap")) # getFasta(ah[[1]], Hsapiens, width = 150, filename = "tmp.fa") # fn <- "tmp.fa" # pred <- getShape(fn) ## ----eval=TRUE---------------------------------------------------------------- library(DNAshapeR) fn_methy <- system.file("extdata", "MethylSample.fa", package = "DNAshapeR") pred_methy <- getShape(fn_methy, methylate = TRUE) pred_methy$MGW ## ----eval=TRUE---------------------------------------------------------------- library(DNAshapeR) fn_methy <- system.file("extdata", "SingleSeqsample.fa", package = "DNAshapeR") fn_methy_pos <- system.file("extdata", "MethylSamplePos.fa", package = "DNAshapeR") pred_methy <- getShape(fn_methy, methylate = TRUE, methylatedPosFile = fn_methy_pos) pred_methy$MGW ## ----fig.width=7, fig.height=7, fig.align='center', eval=TRUE----------------- plotShape(pred$MGW) #plotShape(pred$ProT) #plotShape(pred$Roll) #plotShape(pred$HelT) ## ----fig.width=7, fig.height=7, fig.align='center', eval=TRUE----------------- library(fields) heatShape(pred$ProT, 20) #heatShape(pred$MGW, 20) #heatShape(pred$Roll[1:500, 1:1980], 20) #heatShape(pred$HelT[1:500, 1:1980], 20) ## ----fig.width=7, fig.height=7, fig.align='center', eval=TRUE----------------- fn2 <- system.file("extdata", "SingleSeqsample.fa", package = "DNAshapeR") pred2 <- getShape(fn2) trackShape(fn2, pred2) # Only for single sequence file ## ----eval=TRUE---------------------------------------------------------------- library(Biostrings) fn3 <- system.file("extdata", "PBMsample_short.fa", package = "DNAshapeR") pred3 <- getShape(fn3) featureType <- c("1-mer", "1-shape") featureVector <- encodeSeqShape(fn3, pred3, featureType) head(featureVector) ## ----eval=TRUE---------------------------------------------------------------- fn4 <- system.file("extdata", "PBMsample_short.s", package = "DNAshapeR") experimentalData <- read.table(fn4) df <- data.frame(affinity=experimentalData$V1, featureVector) ## ----eval=TRUE---------------------------------------------------------------- library(caret) trainControl <- trainControl(method = "cv", number = 3, savePredictions = TRUE) model <- train (affinity~ ., data = df, trControl=trainControl, method="lm", preProcess=NULL) model ## ----eval=TRUE---------------------------------------------------------------- sessionInfo()