This function calculates tag clusters from
a RangedSummarizedExperiment object ctss_rse
and extends them by a specified distance ext_dis
around the thick positions.
Usage
plc_get_tcs_and_extend_fromthick(ctss_rse, ext_dis = 200)
Arguments
- ctss_rse
A RangedSummarizedExperiment object containing CAGE data.
- ext_dis
An integer specifying the distance
to extend around thick positions (default is 200).
Value
A GenomicRanges::GRangesList object where each element corresponds to
a tag cluster extended by ext_dis around the thick positions.
Details
The function iterates over columns of ctss_rse,
calculates pooled counts,
subsets clusters based on a score threshold (> 0),
and clusters them unidirectionally.
It then extends each cluster by ext_dis base pairs
around the thick positions
and stores the results in a GRangesList object.
Examples
# Example usage with a RangedSummarizedExperiment object
# ctss_rse <- ... # Load or create your RangedSummarizedExperiment object
# ext_dis <- 200 # Define your extension distance
# result <- get_tagclusters_and_extend_fromthick(ctss_rse, ext_dis)