## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- echo=FALSE, results="hide", warning=FALSE------------------------------- suppressPackageStartupMessages({ library(JASPAR2020) library(TFBSTools) }) ## ----setup-------------------------------------------------------------------- library(JASPAR2020) library(TFBSTools) ## ----example_name_id, tidy=TRUE----------------------------------------------- ## the user assigns a single matrix ID to the argument ID pfm <- getMatrixByID(JASPAR2020, ID="MA0139.1") ## the function returns a PFMatrix object pfm ## ----seq_logo----------------------------------------------------------------- seqLogo(toICM(pfm)) ## ----multiple_matrix_id------------------------------------------------------- ## the user assigns multiple matrix IDs to the argument ID pfmList <- getMatrixByID(JASPAR2020, ID=c("MA0139.1", "MA1102.1")) ## the function returns a PFMatrix object pfmList ## PFMatrixList can be subsetted to extract enclosed PFMatrix objects pfmList[[2]] ## ----getMatrixByName_example-------------------------------------------------- pfm <- getMatrixByName(JASPAR2020, name="Arnt") pfm pfmList <- getMatrixByName(JASPAR2020, name=c("Arnt", "Ahr::Arnt")) pfmList ## ----example_set, tidy=TRUE--------------------------------------------------- ## select all matrices found in a specific species and constructed from the SELEX experiment opts <- list() opts[["species"]] <- 9606 opts[["type"]] <- "SELEX" opts[["all_versions"]] <- TRUE PFMatrixList <- getMatrixSet(JASPAR2020, opts) PFMatrixList ## retrieve all matrices constructed from SELEX experiment opts2 <- list() opts2[["type"]] <- "SELEX" PFMatrixList2 <- getMatrixSet(JASPAR2020, opts2) PFMatrixList2 ## ----session_info, echo=FALSE------------------------------------------------- sessionInfo()