binstats: binstats

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

binstats

Description

Given GRanges of binned eg read depth data with field $cn, crosses nodes in graph and annotates graph nodes with 'cn' and 'weight'. Done upstream of balance.

If "by" field(s) specified and these fields exist in both bins and graph nodes, then will use these in the overlaps query

If field, purity, and ploidy provided then will also transform read depth data in bin column "field" using purity and ploidy to generate

Usage

binstats(
  gg,
  bins,
  by = NULL,
  field = NULL,
  purity = gg$meta$purity,
  ploidy = gg$meta$ploidy,
  loess = TRUE,
  min.bins = 3,
  verbose = TRUE,
  min.var = 0.1,
  lp = FALSE
)

Arguments

gg	gGraph
bins	GRanges with field $cn or field field
by	optional character vector specifying metadata field(s) shared by gg$nodes and bins to which bin / node overlaps will be limited to
field	character vector field of bins to convert to (NULL)
purity	purity parameter either specified together with field or embedded in gg$meta, must be specified if field is not NULL
ploidy	ploidy parameter either specified together with field or embedded in gg$meta, must be specified if field is not NULL
loess	logical flag whether to smooth / fit variance using loess (FALSE)
min.bins	minimum number of bins to use for intra segment variance computation (3)
min.var	minimal allowable per segment bin variance, which will ignore segments with very low variance due to all 0 or other reasons (0.1)
lp	(logical) return weights consistent with LP optimization

Value

gGraph whose nodes are annotated with $cn and $weight field

Author(s)

Marcin Imielinski

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