## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL, ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html warning = FALSE ) ## ----'install', eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("CTCF") ## ----get-data----------------------------------------------------------------- suppressMessages(library(AnnotationHub)) ah <- AnnotationHub() query_data <- query(ah, "CTCF") query_data ## ----------------------------------------------------------------------------- query_data["AH95566"] ## ----------------------------------------------------------------------------- CTCF_hg38 <- query_data[["AH95566"]] CTCF_hg38 ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics("../man/figures/CTCF_hg38_qvalue.png") ## ----------------------------------------------------------------------------- # Check length before filtering length(CTCF_hg38) # Filter and check length after filtering CTCF_hg38 <- CTCF_hg38[CTCF_hg38$q.value < 0.3] length(CTCF_hg38) ## ----eval = FALSE------------------------------------------------------------- # # hg19 CTCF coordinates # CTCF_hg19 <- query_data[["AH95565"]] # # mm9 CTCF coordinates # CTCF_mm9 <- query_data[["AH95567"]] # # mm10 CTCF coordinates # CTCF_mm10 <- query_data[["AH95568"]] ## ----'citation', eval = requireNamespace('CTCF')------------------------------ print(citation("CTCF"), bibtex = TRUE) ## ----reproduce1, echo=FALSE--------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info()