plot_genome_coverage: plot_genome_coverage

In MitoHEAR: Quantification of Mitochondrial DNA Heteroplasmy

plot_genome_coverage

Description

plot_genome_coverage

Usage

plot_genome_coverage(biomart_file, path_fasta, chr_name, heteroplasmy_matrix)

Arguments

biomart_file	Character string with full path to the txt file downloaded from BioMart https://m.ensembl.org/info/data/biomart/index.html . It must have the following five columns:Gene.stable.ID, Gene.name, Gene.start..bp., Gene.end..bp., Chromosome.scaffold.name
path_fasta	Character string with full path to the fasta file of the genomic region of interest. It should be the same file used in get_raw_counts_allele.
chr_name	Character specifying the name of the chromosome of interest. It must be one of the names in the Chromosome.scaffold.name column from the biomart_file.
heteroplasmy_matrix	Third element returned by get_heteroplasmy.

Value

KaryoPlot object as returned by plotKaryotype function from package karyoploteR.

Author(s)

Gabriele Lubatti [e-mail]

See Also

http://bioconductor.org/packages/release/bioc/html/karyoploteR.html

MitoHEAR documentation built on March 18, 2022, 6:47 p.m.