summarizeCircs-methods: load circRNA detection output to a SummarizedExperiment...
In BIMSBbioinfo/ciRcus: Annotation, analysis and visualization of circRNA data

Description Usage Arguments Value

Function that reads an arbitrary number of circRNA lists and returns a SummarizedExperiment object. The resulting object contains unified circ RNA coordinates as GRanges and counts of back-spliced and linearly spliced reads for each circRNA in each sample

summarizeCircs(colData = NULL, keep.linear = TRUE, wobble = 5,
  subs = "all", qualfilter = TRUE, keepCols = 1:6, ...)

## S4 method for signature 'data.frame'
summarizeCircs(colData, keep.linear, wobble, subs,
  qualfilter, keepCols)

## S4 method for signature 'character'
summarizeCircs(colData, keep.linear, wobble, subs,
  qualfilter, keepCols)

`colData`	A `data.frame` object that contains input files and sample names to be used for further analysis. Sample names should be unique characters
`keep.linear`	A boolean indicating whether to keep the counts of linearly spliced transcripts
`wobble`	Number of nucleotides around the splicing border that should be considered when collapsing circular transcripts - helps with mapping imprecision
`subs`	A character string, keep only lines containing it in the name column
`qualfilter`	A boolean. Should quality filtering be performed?
`keepCols`	An integer vector. Which input columns should be returned?
`...`	other arguments