plotGenomicCutouts: plotGenomicCutouts

In markheron/nucular: utility functions used for the analysis of genomic nucleosome data

Description

Create oligonucleotide frequency profile figure from genome positions

Usage

plotGenomicCutouts(pos, strand, size, order, genome, chromosomes,
  sample = 0)

Arguments

pos	ff_list of the nucleosome fragments
strand	list of "+"/"-" vectors
size	in either direction of the dyad position for which to count and plot the oligo frequencies
order	of the oligonucleotides
genome	character string of the folder where the genome fasta files are located, or a DNAStringSet of the genome
chromosomes	which chromosomes to use (must be contained in both genome and pos)
sample	if >0 only use the first sample positions per chromosome

Value

olinucleotide frequency matrix, rows are the oligonucleotides, cols the positions around the dyad

markheron/nucular documentation built on Feb. 18, 2020, 12:32 a.m.