callMotif: Call Motif

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

Call Motif

Description

This function analyzes motifs within DNA sequences based on specified criteria. It supports integration with mutation data and allows for downsampling of reference based (i.e., non-mutant) motifs to balance the dataset.

Usage

callMotif(
  frag_obj,
  motif_type = "s",
  motif_length = 3L,
  integrate_mut = FALSE,
  ref_type = "locus_fragment",
  downsample_ref = FALSE,
  ...
)

Arguments

frag_obj	GRanges object containing DNA fragment information.
motif_type	Character string describing the type of motifs to analyze.
motif_length	An integer specifying the length of the motifs.
integrate_mut	Logical, indicates whether to integrate 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, if TRUE, downsamples reference motifs to match the count of mutant motifs.
...	Additional parameters passed to underlying functions.

Value

Returns a tibble containing the results of the motif analysis.

Examples

callMotif(frag_obj = myData, motif_type = "s",
          motif_length = 2, integrate_mut = TRUE, downsample_ref = FALSE)

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