callLength: Call Fragment Length

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Call Fragment Length

Description

Computes distribution of fragment sizes from BAM/GRanges data. Optionally integrates mutational data, normalizes fragment counts, and adjusts for specific reference types.

Usage

callLength(
  frag_obj,
  isize_min = 1L,
  isize_max = 1000L,
  integrate_mut = FALSE,
  ref_type = "locus_fragment",
  downsample_ref = FALSE,
  ...
)

Arguments

frag_obj	GRanges object containing DNA fragment information.
isize_min	Minimum insert size for filtering (default 1).
isize_max	Maximum insert size for filtering (default 1000).
integrate_mut	Logical, TRUE integrates mutational data.
ref_type	Specifies the type of reference fragments for comparison with MUT fragments: 'locus_fragment' refers to fragments/read-pairs overlapping specific mutation loci, 'outer_fragment' refers to fragments/read-pairs that do not overlap indicated mutation loci.
downsample_ref	Logical, TRUE to match REF and MUT fragment counts.
...	Additional arguments for downstream functions.

Value

Returns a tibble with summarized fragment data, optionally including mutational analysis.

Examples

callLength(frag_obj = myFragData, isize_min = 1L, isize_max = 1000L,
           integrate_mut = TRUE)

hw538/cfDNAPro documentation built on Feb. 17, 2025, 6:09 p.m.