Read, Manipulate and Visualize 'Pairwise mApping Format' Data

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Documentation for package ‘pafr’ version 0.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

as_paf	Coerce a data.frame or tibble into a pafr object
chrom_sizes	Extract the sizes of all sequences in a paf alignment
dotplot	Generate a dot plot from a paf alignment
filter_secondary_alignments	Remove secondary alignments from a pafr alignment
Gb_lab	Number formatters for scales in base pairs
highlight_query	Highlight segments of a query or target genome in a dot plot
highlight_target	Highlight segments of a query or target genome in a dot plot
Kb_lab	Number formatters for scales in base pairs
Mb_lab	Number formatters for scales in base pairs
plot_coverage	Plot the regions of one genome that are covered by alignments in a paf file
plot_synteny	Plot synteny between a query and target sequence in a PAF alignment
read_bed	Read genomic intervals in bed format
read_paf	Read a genomic alignment in PAF format
theme_coverage_plot	A minimalistic ggplot2 theme designed for use with genome coverage plots