miga-base 0.4.3.0 → 0.5.0.0

data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd

@@ -1,24 +1,29 @@
-\name{enve.recplot2.coordinates}
-\alias{enve.recplot2.coordinates}
-\title{enve recplot2 coordinates}
-\description{Returns the sequence name and coordinates of the requested position bins.}
-\usage{enve.recplot2.coordinates(x, bins)}
-\arguments{
-  \item{x}{`enve.RecPlot2` object.}
-  \item{bins}{Vector of selected bins to return. It can be a vector of logical values
-with the same length as `x$pos.breaks`-1 or a vector of integers. If
-missing, returns the coordinates of all windows.}
-}
-
-\value{Returns a data.frame with four columns: name.from (character), pos.from
-(numeric) name.to (character), and pos.to (numeric). The first two
-correspond to sequence and position of the start point of the bin, the
-last two correspond to the sequence and position of the end point of the
-bin.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.coordinates}
+\alias{enve.recplot2.coordinates}
+\title{Enveomics: Recruitment Plot (2) Coordinates}
+\usage{
+enve.recplot2.coordinates(x, bins)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object.}
+
+\item{bins}{Vector of selected bins to return. It can be a vector of logical values
+with the same length as \code{x$pos.breaks-1} or a vector of integers. If
+missing, returns the coordinates of all windows.}
+}
+\value{
+Returns a data.frame with five columns: \code{name.from} (character),
+\code{pos.from} (numeric), \code{name.to} (character), \code{pos.to}
+(numeric), and \code{seq.name} (character).
+The first two correspond to sequence and position of the start point of the
+bin. The next two correspond to the sequence and position of the end point of
+the bin. The last one indicates the name of the sequence (if defined).
+}
+\description{
+Returns the sequence name and coordinates of the requested position bins.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd

@@ -1,18 +1,18 @@
-\name{enve.recplot2.corePeak}
-\alias{enve.recplot2.corePeak}
-\title{enve recplot2 corePeak}
-\description{Finds the peak in a list of peaks that is most likely to represent the
-"core genome" of a population.}
-\usage{enve.recplot2.corePeak(x)}
-\arguments{
-  \item{x}{`list` of `enve.RecPlot2.Peak` objects.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.corePeak}
+\alias{enve.recplot2.corePeak}
+\title{Enveomics: Recruitment Plot (2) Core Peak Finder}
+\usage{
+enve.recplot2.corePeak(x)
+}
+\arguments{
+\item{x}{\code{list} of \code{\link{enve.RecPlot2.Peak}} objects.}
+}
+\description{
+Finds the peak in a list of peaks that is most likely to represent the
+"core genome" of a population.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd

@@ -1,34 +1,40 @@
-\name{enve.recplot2.extractWindows}
-\alias{enve.recplot2.extractWindows}
-\title{enve recplot2 extractWindows}
-\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{
-  \item{rp}{Recruitment plot, a `enve.RecPlot2` object.}
-  \item{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`).}
-  \item{lower.tail}{If FALSE, it returns windows significantly above the peak in
-sequencing depth.}
-  \item{significance}{Significance threshold (alpha) to select windows.}
-  \item{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 vector of characters if the object has `pos.names` defined,
-or a data.frame with four columns otherwise:
-name.from, name.to, pos.from, and pos.to
-(see `enve.recplot2.coordinates`).}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.extractWindows}
+\alias{enve.recplot2.extractWindows}
+\title{Enveomics: Recruitment Plot (2) Extract Windows}
+\usage{
+enve.recplot2.extractWindows(rp, peak, lower.tail = TRUE,
+  significance = 0.05, seq.names = FALSE)
+}
+\arguments{
+\item{rp}{Recruitment plot, a \code{\link{enve.RecPlot2}} object.}
+
+\item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
+list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
+used (see \code{\link{enve.recplot2.corePeak}}).}
+
+\item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
+sequencing depth.}
+
+\item{significance}{Significance threshold (alpha) to select windows.}
+
+\item{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
+\code{pos.breaks=0} or a two-column \code{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 \code{seq.names = FALSE}.
+If \code{seq.names = TRUE}, it returns a data.frame with five columns:
+\code{name.from}, \code{name.to}, \code{pos.from}, \code{pos.to}, and
+\code{seq.name} (see \code{\link{enve.recplot2.coordinates}}).
+}
+\description{
+Extract windows significantly below (or above) the peak in sequencing
+depth.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd

@@ -1,24 +1,36 @@
-\name{enve.recplot2.findPeaks}
-\alias{enve.recplot2.findPeaks}
-\title{enve recplot2 findPeaks}
-\description{Identifies peaks in the population histogram potentially indicating
-sub-population mixtures}
-\usage{enve.recplot2.findPeaks(x, method = "emauto", ...)}
-\arguments{
-  \item{x}{An `enve.RecPlot2` object.}
-  \item{method}{Peak-finder method. This should be one of:
-"emauto" (Expectation-Maximization with auto-selection of components),
-"em" (Expectation-Maximization),
-"mower" (Custom distribution-mowing method).}
-  \item{\dots}{Any additional parameters supported by
-`enve.recplot2.findPeaks.<method>`.}
-}
-
-\value{Returns a list of `enve.RecPlot2.Peak` objects.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks}
+\alias{enve.recplot2.findPeaks}
+\title{Enveomics: Recruitment Plot (2) Peak Finder}
+\usage{
+enve.recplot2.findPeaks(x, method = "emauto", ...)
+}
+\arguments{
+\item{x}{An \code{\link{enve.RecPlot2}} object.}
+
+\item{method}{Peak-finder method. This should be one of:
+\itemize{
+   \item \strong{emauto}
+   (Expectation-Maximization with auto-selection of components)
+   \item \strong{em}
+   (Expectation-Maximization)
+   \item \strong{mower}
+   (Custom distribution-mowing method)
+}}
+
+\item{...}{Any additional parameters supported by
+\code{\link{enve.recplot2.findPeaks}}.}
+}
+\value{
+Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
+}
+\description{
+Identifies peaks in the population histogram potentially indicating
+sub-population mixtures.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+
+export
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd

@@ -1,20 +1,19 @@
-\name{enve.recplot2.findPeaks.__em_e}
-\alias{enve.recplot2.findPeaks.__em_e}
-\title{enve recplot2 findPeaks   em e}
-\description{Internal ancilliary function (see `enve.recplot2.findPeaks.em`).}
-\usage{enve.recplot2.findPeaks.__em_e(x, theta)}
-\arguments{
-  \item{x}{
-}
-  \item{theta}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.__em_e}
+\alias{enve.recplot2.findPeaks.__em_e}
+\title{Enveomics: Recruitment Plot (2) EM Peak Finder - Internal Ancillary Function Expectation}
+\usage{
+enve.recplot2.findPeaks.__em_e(x, theta)
+}
+\arguments{
+\item{x}{Vector of log-transformed sequencing depths}
+
+\item{theta}{Parameters list}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd

@@ -1,20 +1,19 @@
-\name{enve.recplot2.findPeaks.__em_m}
-\alias{enve.recplot2.findPeaks.__em_m}
-\title{enve recplot2 findPeaks   em m}
-\description{Internal ancilliary function (see `enve.recplot2.findPeaks.em`}
-\usage{enve.recplot2.findPeaks.__em_m(x, posterior)}
-\arguments{
-  \item{x}{
-}
-  \item{posterior}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.__em_m}
+\alias{enve.recplot2.findPeaks.__em_m}
+\title{Enveomics: Recruitment Plot (2) Em Peak Finder - Internal Ancillary Function Maximization}
+\usage{
+enve.recplot2.findPeaks.__em_m(x, posterior)
+}
+\arguments{
+\item{x}{Vector of log-transformed sequencing depths}
+
+\item{posterior}{Posterior probability}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd

@@ -1,29 +1,27 @@
-\name{enve.recplot2.findPeaks.__emauto_one}
-\alias{enve.recplot2.findPeaks.__emauto_one}
-\title{enve recplot2 findPeaks   emauto one}
-\description{Internal ancilliary function (see `enve.recplot2.findPeaks.emauto).}
-\usage{enve.recplot2.findPeaks.__emauto_one(x, comp, do_crit, best, 
-    verbose, ...)}
-\arguments{
-  \item{x}{
-}
-  \item{comp}{
-}
-  \item{do_crit}{
-}
-  \item{best}{
-}
-  \item{verbose}{
-}
-  \item{\dots}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.__emauto_one}
+\alias{enve.recplot2.findPeaks.__emauto_one}
+\title{Enveomics: Recruitment Plot (2) EMauto Peak Finder - Internal Ancillary Function}
+\usage{
+enve.recplot2.findPeaks.__emauto_one(x, comp, do_crit, best, verbose, ...)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object}
+
+\item{comp}{Components}
+
+\item{do_crit}{Function estimating the criterion}
+
+\item{best}{Best solution thus far}
+
+\item{verbose}{If verbose}
+
+\item{...}{Additional parameters for \code{\link{enve.recplot2.findPeaks.em}}}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.emauto}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd

@@ -1,42 +1,41 @@
-\name{enve.recplot2.findPeaks.__mow_one}
-\alias{enve.recplot2.findPeaks.__mow_one}
-\title{enve recplot2 findPeaks   mow one}
-\description{Internall ancilliary function (see `enve.recplot2.findPeaks.mower`).}
-\usage{enve.recplot2.findPeaks.__mow_one(lsd1, min.points, quant.est, 
-    mlv.opts, fitdist.opts, with.skewness, optim.rounds, optim.epsilon, 
-    n.total, merge.logdist, verbose, log)}
-\arguments{
-  \item{lsd1}{
-}
-  \item{min.points}{
-}
-  \item{quant.est}{
-}
-  \item{mlv.opts}{
-}
-  \item{fitdist.opts}{
-}
-  \item{with.skewness}{
-}
-  \item{optim.rounds}{
-}
-  \item{optim.epsilon}{
-}
-  \item{n.total}{
-}
-  \item{merge.logdist}{
-}
-  \item{verbose}{
-}
-  \item{log}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.__mow_one}
+\alias{enve.recplot2.findPeaks.__mow_one}
+\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1}
+\usage{
+enve.recplot2.findPeaks.__mow_one(lsd1, min.points, quant.est, mlv.opts,
+  fitdist.opts, with.skewness, optim.rounds, optim.epsilon, n.total,
+  merge.logdist, verbose, log)
+}
+\arguments{
+\item{lsd1}{Vector of log-transformed sequencing depths}
+
+\item{min.points}{Minimum number of points}
+
+\item{quant.est}{Quantile estimate}
+
+\item{mlv.opts}{List of options for \code{mlv}}
+
+\item{fitdist.opts}{List of options for \code{fitdist}}
+
+\item{with.skewness}{If skewed-normal should be used}
+
+\item{optim.rounds}{Maximum number of optimization rounds}
+
+\item{optim.epsilon}{Minimum difference considered negligible}
+
+\item{n.total}{Global number of windows}
+
+\item{merge.logdist}{Attempted \code{merge.logdist} parameter}
+
+\item{verbose}{If verbose}
+
+\item{log}{If log-transformed depths}
+}
+\description{
+Internall ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}