## ----load MotifDb, query CTCF, prompt=FALSE, message=FALSE, results="show"---- library(MotifDb) query(MotifDb, "ctcf") ## ----query CTCF human, prompt=FALSE, message=FALSE, results="show"------------ library(MotifDb) motifs <- query(MotifDb, andStrings=c("CTCF", "hsapiens"), orStrings=c("jaspar2018", "hocomocov11-core-A"), notStrings="ctcfl") length(motifs) ## ----compare CTCF motifs, prompt=FALSE, message=FALSE, results="show"--------- sapply(motifs, consensusString) ## ----use seqLogo, prompt=FALSE, message=FALSE, results="hide", fig.width = 5, fig.height = 5, fig.show = "hold", out.width = "50%"---- library(seqLogo) seqLogo(motifs[[1]]) # Hsapiens-jaspar2018-CTCF-MA0139.1 seqLogo(motifs[[2]]) # Hsapiens-HOCOMOCOv11-core-A-CTCF_HUMAN.H11MO.0.A ## ----ChIP-vs-FIMO, eval=TRUE, echo=FALSE-------------------------------------- knitr::include_graphics("GSM749704-CTCF-chipVsFimo.png")