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Filter out common germline copy-number variants

filter_blacklist.Rd

Filter out common germline copy-number variants

Usage

filter_blacklist(
  probe_info,
  blacklist = "hg38",
  start_col = "flanking.start",
  end_col = "flanking.end"
)

Arguments

probe_info

Tibble or filepath to a text file containing probe information. Should have a "locus" column of the following form: "{chr}:{start}-{end}" where {chr} is 1-22, X, or Y and where {start} and {end} are genomic coordinates

blacklist

By default hg38. If the data in probe_info is aligned to hg19, set this parameter to "hg19". A dataframe or filepath can also be supplied as a parameter for custom filtering. Blacklist should have a chr column with chromosome names (1-22, X, or Y) and columns for start and end coordinates.

start_col

The name of the column in the blacklist file to use as the start coordinate for filtering

end_col

The name of the column in the blacklist file to use as the end coordinate for filtering

Value

Input probe_info dataframe with rows overlapping the blacklist removed