## ---- include=FALSE----------------------------------------------------------- library(BiocStyle) ## ----echo=FALSE, out.width="35%", fig.align = 'center'------------------------ knitr::include_graphics(system.file('docs', '12mer.png', package = 'scanMiR')) ## ----------------------------------------------------------------------------- library(scanMiR) data(SampleKdModel) SampleKdModel ## ----------------------------------------------------------------------------- SampleKdModel$myVariable <- "test" ## ----------------------------------------------------------------------------- plotKdModel(SampleKdModel, what="seeds") ## ----------------------------------------------------------------------------- assignKdType("ACGTACGTACGT", SampleKdModel) # or using multiple sequences: assignKdType(c("CTAGCATTAAGT","ACGTACGTACGT"), SampleKdModel) ## ----------------------------------------------------------------------------- # we create a copy of the KdModel, and give it a different name: mod2 <- SampleKdModel mod2$name <- "dummy-miRNA" kml <- KdModelList(SampleKdModel, mod2) kml summary(kml) ## ----------------------------------------------------------------------------- conservation(kml) ## ----------------------------------------------------------------------------- kd <- dummyKdData() head(kd) ## ----------------------------------------------------------------------------- mod3 <- getKdModel(kd=kd, mirseq="TTAATGCTAATCGTGATAGGGGTT", name = "my-miRNA") ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()