circSample: S4 class for storing circRNA relevant information.
In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data

S4 class for storing circRNA relevant information.

circSample-object

sample.id: The id of the sample, specified by the input sample file naming (e.g. 'aligned/[sample]/Chimeric.out.junction', where '[sample]' are the applied id.), 'sample.id“. Must be unique!
organism: The organism of which the smaple originates from.
gb: The specific genome build used for alining the sample.
chim.file: File location for the sample 'Chimeric.out.junction' alignment output.
bam.file: File locaion for the sample 'Aligned.X.out.bam' alignment output, where X specifies a sorting option during alignment by the STAR algorithm. #[PROPPER REFS?]
log.file: File location for the sample 'Log.final.out' alignment run log.
sj.file: File location for the sample 'SJ.out.tab' alignment output.
firstread.firststrand: Library preparation protocol, relative to library strandedness. If a first_read-first_strand protocol is used (e.g. dUTP), then 'firstread.firststrand' is 'TRUE', if first_read-second_strand or unstranded then it is 'FALSE'.
paired.end: Flag used for describing if whether the sample sequnecing data are paired-end or single-end. Must be logical!
bsj.reads: Annotated and shifted candidate junctions
bsj.counts: The number of reads covering a backsplice junction for each detected basckplice junction CANDIDATES?.
lsj.counts: The input linear splice junction data.
label: An optional name for a given sample, if no 'label' is provided, 'sample.id“ will be used. Need to check if labels are unique when constructing an experiment!!!!

circSample(
    sample.id = "A549",
    organism = "Homo sapiens",
    gb = "hg38",
    chim.file = "Chimeric.out.junction",
    bam.file = "Aligned.sortedByCoord.out.bam",
    log.file = "Log.final.out",
    sj.file = "SJ.out.tab",
    firstread.firststrand = TRUE,
    paired.end = TRUE
)