| plot_genome_coverage {MitoHEAR} | R Documentation |
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 gabriele.lubatti@helmholtz-muenchen.de
See Also
http://bioconductor.org/packages/release/bioc/html/karyoploteR.html