Get CN Segments.
get_cn_segments.Rd
Retrieve all copy number segments from the GAMBL outputs
Arguments
- these_samples_metadata
User must provide a metadata table to restrict the data to the samples in your table. The metadata also ensures the proper handling of duplicate sample_id across seq_types and ensures the seq_type in the metadata faithfully represents the seq_type of the data
- projection
Desired genome coordinate system for returned CN segments. Default is "grch37".
- this_seq_type
Deprecated.
- ...
Additional parameters to be passed to the function.
Details
This function merely loads and returns all the seg_data available for a projection (genome build)
Examples
# Example for the capture samples:
genome_metadata = get_gambl_metadata(seq_type_filter="genome")
#> Using the bundled metadata in GAMBLR.data...
genome_segments_hg38 = get_cn_segments(
these_samples_metadata = genome_metadata,
projection="hg38")
#> Using the bundled CN segments (.seg) calls in GAMBLR.data...