GeneratePlotPFMmatrix: Generate PFMmatrix (Position Frequency Matrix) from a given...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Generate PFMmatrix (Position Frequency Matrix) from a given list of sequences

Description

Generate PFMmatrix (Position Frequency Matrix) from a given list of sequences

Usage

GeneratePlotPFMmatrix(
  sequences,
  indel.class,
  flank.length = 5,
  plot.dir = NULL,
  plot.title = NULL
)

Arguments

sequences	A list of strings returned from SymmetricalContextsFor1BPIndel.
indel.class	A single character string that denotes a 1 base pair insertion or deletion, as taken from ICAMS::catalog.row.order$ID. Insertions or deletions into or from 5+ base-pair homopolymers are not supported.
flank.length	The length of flanking bases around the position or homopolymer targeted by the indel.
plot.dir	If provided, make a dot-line plot for PFMmatrix.
plot.title	The title of the dot-line plot

Value

A matrix recording the frequency of each base (A, C, G, T) on each position of the sequence.

ICAMS documentation built on June 15, 2025, 1:08 a.m.