## ----style, echo=FALSE, results="asis", message=FALSE------------------------- knitr::opts_chunk$set(tidy = FALSE, message = FALSE) ## ----echo=FALSE--------------------------------------------------------------- CRANpkg <- function (pkg) { cran <- "https://CRAN.R-project.org/package" fmt <- "[%s](%s=%s)" sprintf(fmt, pkg, cran, pkg) } Biocpkg <- function (pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } ## ----echo=FALSE, results='hide', message=FALSE-------------------------------- library(FScanR) ## ----eval = FALSE------------------------------------------------------------- # ## Install FScanR in R (>= 3.5.0) # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("FScanR") ## ----------------------------------------------------------------------------- ## loading package library(FScanR) ## loading test data test_data <- read.table(system.file("extdata", "test.tab", package = "FScanR"), header=TRUE, sep="\t") ## ----------------------------------------------------------------------------- ## loading packages prf <- FScanR(test_data, evalue_cutoff = 1e-05, frameDist_cutoff = 10) table(prf$FS_type) ## ----------------------------------------------------------------------------- ## plot the 4-type PRF events detected mytable <- table(prf$FS_type) lbls <- paste(names(mytable), " : ", mytable, sep="") pie(mytable, labels = NA, main=paste0("PRF events"), cex=0.5, col=cm.colors(length(mytable))) legend("right",legend=lbls[!is.na(lbls)], bty="n", cex=1, fill=cm.colors(length(mytable))[!is.na(lbls)]) ## ----echo=FALSE--------------------------------------------------------------- sessionInfo()