callTrinucleotide: Call trinucleotides and summarise the cfDNA information for...

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

Call trinucleotides and summarise the cfDNA information for each target mutation locus.

Description

This function processes a GRanges object, summarizing cfDNA fragment information for each target mutation locus.

Usage

callTrinucleotide(frag_obj_mut)

Arguments

frag_obj_mut

GRanges object containing fragment and mutation data.

Details

It annotates each mutation locus with the number and type of supporting fragments according to their read-pair overlap status.

The median fragment length is also annotated for each read-pair overlap type.

Locus-based consensus mutation is determined by selecting the most frequent mismatch type, with priority given to concordant read-pair mutations (CO_MUT) followed by single-read mutations (SO_MUT). The consensus mutations are then used to derive the trinucleotide substitution types (SBS96).

Value

dataframe with summarised mutational and trinucleotide data.

Examples

trinuc_df <-  callTrinucleotide(frag_obj_mut)

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