peel: peel

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

peel

Description

Greedily "peels" walks off a genome graph with node and edge field "cn" by finding successive flows that maximizes some edge metadata field (specified as field) which if not specified will be a logical field type == 'ALT' specifying whether that junction is an ALT edge

Usage

peel(gg, field = NULL, embed.loops = FALSE, verbose = FALSE, cache.path = NULL)

Arguments

gg	gGraph with field cn
field	edge metadata field to use to rank walk solutions (default edge field type == 'ALT')s
embed.loops	logical flag (FALSE) if TRUE will embed all the loops in the output into an arbitrary linear (path) walk
verbose	flag = 1 regular verbosity, 2 = dump out Rcplex traces

Value

collection of gWalks annotated with cn on the original that when added will give the marginal copy profile on inputted nodes and edges

Author(s)

Marcin Imielinski

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.