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Retrieve all copy number segments from the GAMBL outputs

Usage

get_cn_segments(
  these_samples_metadata,
  projection = "grch37",
  this_seq_type,
  ...
)

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.

Value

A data frame with CN segments for the specified region.

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...