ampliconParams: Lists germline filters and parameters for filtering amplicons

In cancer-genomics/trellis: Somatic structural variant analysis

Lists germline filters and parameters for filtering amplicons

Description

Lists germline filters and parameters for filtering amplicons

Usage

ampliconParams(
  AMP_THR = log2(2.75),
  LOW_THR = log2(1.75),
  border_size = 10000,
  overhang = 25000,
  MIN_WIDTH = 2000,
  MIN_SEGMEAN_DIFF = 0.05,
  min.gapwidth = 3000,
  maxgap = 5e+05,
  frequency = 5,
  minimum_maxdist = 50,
  minimum_count = 5,
  bad_bins = GRanges()
)

Arguments

AMP_THR	numeric threshold for high copy amplicon
LOW_THR	numeric a lower threshold used when considering amplicons that are bridged by improper read pairs to a high copy amplicon
border_size	used to construct a query (GRanges object) for additional amplicons neighboring a focal amplicon. TODO: more detail needed.
overhang	An integer indicating how much to expand the germline filter on each size. Using overlapsAny, a determination is made whether an amplicon is part-germline (any overlap) or no-germline (no overlap). If the amplicon is completely within the extended germline filter, the amplicon is considered fully-germline.
MIN_WIDTH	length-one integer vector indicating the minimum size of amplicon (see also joinNearGRanges)
MIN_SEGMEAN_DIFF	length-one numeric vector. Adjacent segments whose means differ by less than this value are candidates for merging by {joinNearGRanges}
min.gapwidth	length-one numeric vector passed to the reduce method that merges adacent segments with comparable segment means
maxgap	length-one numeric vector. Passed to findOverlaps when evaluating whether the amplicon ranges overlap with other amplicons (see linkNearAmplicons).
frequency	minimum number of read pairs
minimum_maxdist	TODO
minimum_count	a length-one integer vector: minimum number of improperly paired reads required to link two amplicons
bad_bins	a GRanges object of problematic bins

Value

Returns a list of germline filters and some of the hard thresholds used in the amplicon analysis.

Examples

params <- ampliconParams("hg19")

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.