enve.recplot2.extractWindows: Enveomics: Recruitment Plot (2) Extract Windows

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Recruitment Plot (2) Extract Windows

Description

Extract windows significantly below (or above) the peak in sequencing depth.

Usage

enve.recplot2.extractWindows(
  rp,
  peak,
  lower.tail = TRUE,
  significance = 0.05,
  seq.names = FALSE
)

Arguments

rp	Recruitment plot, a enve.RecPlot2 object.
peak	Peak, an enve.RecPlot2.Peak object. If list, it is assumed to be a list of enve.RecPlot2.Peak objects, in which case the core peak is used (see enve.recplot2.corePeak).
lower.tail	If FALSE, it returns windows significantly above the peak in sequencing depth.
significance	Significance threshold (alpha) to select windows.
seq.names	Returns subject sequence names instead of a vector of Booleans. If the recruitment plot was generated with named position bins (e.g, using pos.breaks=0 or a two-column pos.breaks.tsv), it returns a vector of characters (the sequence identifiers), otherwise it returns a data.frame with a name column and two columns of coordinates.

Value

Returns a vector of logicals if seq.names = FALSE. If seq.names = TRUE, it returns a data.frame with five columns: name.from, name.to, pos.from, pos.to, and seq.name (see enve.recplot2.coordinates).

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on April 13, 2022, 5:10 p.m.