enve.recplot2.extractWindows {enveomics.R}

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]