ciRcus is a package for easy summarization and exploration of circ RNAs detected in multiple experiments.
library(ciRcus)
The main summarization function in \code{ciRcus} is the \code{summarizeCircs} function. The function takes as input a data.frame which contains minimally 2 columns: 1. sample - sample designation for each file 2. filename - a path to the detected Circ RNAs.
Alternatively, the user can specify supply to the function just the paths to the files, and the coldata will be constructed automatically.
circ.files = list.files(system.file('extdata', package='ciRcus'), pattern='sites.bed', full.names=TRUE) circ.files = circ.files[!grepl('Sy5y', circ.files)] coldata = data.frame(sample = sub('.bed','',basename(circ.files)), file=circ.files) circs = summarizeCircs(coldata) circs
circs = AnnotatateCircs(circs) circs
histogram(circs)
histogram(circs)
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