Convert segmentation GenomicRanges object to a data.table with standardized columns and format

Converts a segmentation GenomicRanges object into a data.table object then extracts the appropriate columns and renames the columns to match the expected format.

The input GenomicRanges is typically generated from get_fragcounter_segmentation() workflow or other DNAcopy CBS algorithm runs.

Usage

gr_to_seg(input_gr, exp_colnames = c("ID", "num.mark", "seg.mean"))

Arguments

input_gr

Segmentation GenomicRanges object to convert to data.table

exp_colnames

Expected column names for CBS segmentation input GenomicRanges

Value

data.table

Examples

# Convert output from `get_fragcounter_segmentation()` workflow
# frag_seg <- get_fragcounter_segmentation(
# path_to_fragcounter_profile = "read_depth_demo_hg38.rds",
# cpus = 4)

# gr_to_seg(dryclean_seg)