miga-base 0.7.24.0 → 0.7.26.0

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

@@ -1,27 +0,0 @@
-% 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

@@ -1,41 +0,0 @@
-% 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]
-}

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

@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.findPeaks.__mower}
-\alias{enve.recplot2.findPeaks.__mower}
-\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 2}
-\usage{
-enve.recplot2.findPeaks.__mower(peaks.opts)
-}
-\arguments{
-\item{peaks.opts}{List of options for \code{\link{enve.recplot2.findPeaks.__mow_one}}}
-}
-\description{
-Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,43 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.findPeaks.em}
-\alias{enve.recplot2.findPeaks.em}
-\title{Enveomics: Recruitment Plot (2) Em Peak Finder}
-\usage{
-enve.recplot2.findPeaks.em(x, max.iter = 1000, ll.diff.res = 1e-08,
-  components = 2, rm.top = 0.05, verbose = FALSE, init, log = TRUE)
-}
-\arguments{
-\item{x}{An \code{\link{enve.RecPlot2}} object.}
-
-\item{max.iter}{Maximum number of EM iterations.}
-
-\item{ll.diff.res}{Maximum Log-Likelihood difference to be considered as convergent.}
-
-\item{components}{Number of distributions assumed in the mixture.}
-
-\item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
-This step is useful to remove highly conserved regions, but can be
-turned off by setting \code{rm.top=0}. The quantile is determined
-\strong{after} removing zero-coverage windows.}
-
-\item{verbose}{Display (mostly debugging) information.}
-
-\item{init}{Initialization parameters. By default, these are derived from k-means
-clustering. A named list with vectors for \code{mu}, \code{sd}, and
-\code{alpha}, each of length \code{components}.}
-
-\item{log}{Logical value indicating if the estimations should be performed in
-natural logarithm units. Do not change unless you know what you're
-doing.}
-}
-\value{
-Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-}
-\description{
-Identifies peaks in the population histogram using a Gaussian Mixture
-Model Expectation Maximization (GMM-EM) method.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,37 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.findPeaks.emauto}
-\alias{enve.recplot2.findPeaks.emauto}
-\title{Enveomics: Recruitment Plot (2) Emauto Peak Finder}
-\usage{
-enve.recplot2.findPeaks.emauto(x, components = seq(1, 5),
-  criterion = "aic", merge.tol = 2L, verbose = FALSE, ...)
-}
-\arguments{
-\item{x}{An \code{\link{enve.RecPlot2}} object.}
-
-\item{components}{A vector of number of components to evaluate.}
-
-\item{criterion}{Criterion to use for components selection. Must be one of:
-\code{aic} (Akaike Information Criterion), \code{bic} or \code{sbc}
-(Bayesian Information Criterion or Schwarz Criterion).}
-
-\item{merge.tol}{When attempting to merge peaks with very similar sequencing depth, use
-this number of significant digits (in log-scale).}
-
-\item{verbose}{Display (mostly debugging) information.}
-
-\item{...}{Any additional parameters supported by
-\code{\link{enve.recplot2.findPeaks.em}}.}
-}
-\value{
-Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-}
-\description{
-Identifies peaks in the population histogram using a Gaussian Mixture
-Model Expectation Maximization (GMM-EM) method with number of components
-automatically detected.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,74 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.findPeaks.mower}
-\alias{enve.recplot2.findPeaks.mower}
-\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder}
-\usage{
-enve.recplot2.findPeaks.mower(x, min.points = 10, quant.est = c(0.002,
-  0.998), mlv.opts = list(method = "parzen"),
-  fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1,
-  0.5, 0.8), start = list(omega = 1, alpha = -1), lower = c(0, -Inf,
-  -Inf)), fitdist.opts.norm = list(distr = "norm", method = "qme", probs
-  = c(0.4, 0.6), start = list(sd = 1), lower = c(0, -Inf)),
-  rm.top = 0.05, with.skewness = TRUE, optim.rounds = 200,
-  optim.epsilon = 1e-04, merge.logdist = log(1.75), verbose = FALSE,
-  log = TRUE)
-}
-\arguments{
-\item{x}{An \code{\link{enve.RecPlot2}} object.}
-
-\item{min.points}{Minimum number of points in the quantile-estimation-range
-\code{(quant.est)} to estimate a peak.}
-
-\item{quant.est}{Range of quantiles to be used in the estimation of a peak's
-parameters.}
-
-\item{mlv.opts}{Ignored. For backwards compatibility.}
-
-\item{fitdist.opts.sn}{Options passed to \code{fitdist} to estimate the standard deviation if
-\code{with.skewness=TRUE}. Note that the \code{start} parameter will be
-ammended with \code{xi=estimated} mode for each peak.}
-
-\item{fitdist.opts.norm}{Options passed to \code{fitdist} to estimate the standard deviation if
-\code{with.skewness=FALSE}. Note that the \code{start} parameter will be
-ammended with \code{mean=estimated} mode for each peak.}
-
-\item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
-This step is useful to remove highly conserved regions, but can be
-turned off by setting \code{rm.top=0}. The quantile is determined
-\strong{after} removing zero-coverage windows.}
-
-\item{with.skewness}{Allow skewness correction of the peaks. Typically, the
-sequencing-depth distribution for a single peak is left-skewed, due
-partly (but not exclusively) to fragmentation and mapping sensitivity.
-See \emph{Lindner et al 2013, Bioinformatics 29(10):1260-7} for an
-alternative solution for the first problem (fragmentation) called
-"tail distribution".}
-
-\item{optim.rounds}{Maximum rounds of peak optimization.}
-
-\item{optim.epsilon}{Trace change at which optimization stops (unless \code{optim.rounds} is
-reached first). The trace change is estimated as the sum of square
-differences between parameters in one round and those from two rounds
-earlier (to avoid infinite loops from approximation).}
-
-\item{merge.logdist}{Maximum value of \code{|log-ratio|} between centrality parameters in peaks
-to attempt merging. The default of ~0.22 corresponds to a maximum
-difference of 25\%.}
-
-\item{verbose}{Display (mostly debugging) information.}
-
-\item{log}{Logical value indicating if the estimations should be performed in
-natural logarithm units. Do not change unless you know what you're
-doing.}
-}
-\value{
-Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-}
-\description{
-Identifies peaks in the population histogram potentially indicating
-sub-population mixtures, using a custom distribution-mowing method.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd

@@ -1,59 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\docType{class}
-\name{enve.RecPlot2.Peak-class}
-\alias{enve.RecPlot2.Peak-class}
-\alias{enve.RecPlot2.Peak}
-\title{Enveomics: Recruitment Plot (2) Peak - S4 Class}
-\description{
-Enve-omics representation of a peak in the sequencing depth histogram
-of a Recruitment plot (see \code{\link{enve.recplot2.findPeaks}}).
-}
-\section{Slots}{
-
-\describe{
-\item{\code{dist}}{\code{(character)}
-Distribution of the peak. Currently supported: \code{norm} (normal) and \code{sn}
-(skew-normal).}
-
-\item{\code{values}}{\code{(numeric)}
-Sequencing depth values predicted to conform the peak.}
-
-\item{\code{values.res}}{\code{(numeric)}
-Sequencing depth values not explained by this or previously identified
-peaks.}
-
-\item{\code{mode}}{\code{(numeric)}
-Seed-value of mode anchoring the peak.}
-
-\item{\code{param.hat}}{\code{(list)}
-Parameters of the distribution. A list of two values if dist=\code{norm} (sd
-and mean), or three values if dist=\code{sn}(omega=scale, alpha=shape, and
-xi=location). Note that the "dispersion" parameter is always first and
-the "location" parameter is always last.}
-
-\item{\code{n.hat}}{\code{(numeric)}
-Number of bins estimated to be explained by this peak. This should
-ideally be equal to the length of  \code{values}, but it's not an integer.}
-
-\item{\code{n.total}}{\code{(numeric)}
-Total number of bins from which the peak was extracted. I.e., total
-number of position bins with non-zero sequencing depth in the recruitment
-plot (regardless of peak count).}
-
-\item{\code{err.res}}{\code{(numeric)}
-Error left after adding the peak (mower) or log-likelihood (em or emauto).}
-
-\item{\code{merge.logdist}}{\code{(numeric)}
-Attempted \code{merge.logdist} parameter.}
-
-\item{\code{seq.depth}}{\code{(numeric)}
-Best estimate available for the sequencing depth of the peak (centrality).}
-
-\item{\code{log}}{\code{(logical)}
-Indicates if the estimation was performed in natural logarithm space.}
-}}
-
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.seqdepth}
-\alias{enve.recplot2.seqdepth}
-\title{Enveomics: Recruitment Plot (2) Sequencing Depth}
-\usage{
-enve.recplot2.seqdepth(x, sel, low.identity = FALSE)
-}
-\arguments{
-\item{x}{\code{\link{enve.RecPlot2}} object.}
-
-\item{sel}{Window(s) for which the sequencing depth is to be calculated. If not
-passed, it returns the sequencing depth of all windows.}
-
-\item{low.identity}{A logical indicating if the sequencing depth is to be estimated only
-with low-identity matches. By default, only high-identity matches are
-used.}
-}
-\value{
-Returns a numeric vector of sequencing depths (in bp/bp).
-}
-\description{
-Calculate the sequencing depth of the given window(s).
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{enve.recplot2.windowDepthThreshold}
-\alias{enve.recplot2.windowDepthThreshold}
-\title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
-\usage{
-enve.recplot2.windowDepthThreshold(rp, peak, lower.tail = TRUE,
-  significance = 0.05)
-}
-\arguments{
-\item{rp}{Recruitment plot, an \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.}
-}
-\value{
-Returns a float. The units are depth if the peaks were estimated in
-linear scale, or log-depth otherwise (\code{peak$log}).
-}
-\description{
-Identifies the threshold below which windows should be identified as
-variable or absent.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.tribs.Rd

@@ -1,59 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tribs.R
-\name{enve.tribs}
-\alias{enve.tribs}
-\title{Enveomics: TRIBS}
-\usage{
-enve.tribs(dist, selection = labels(dist), replicates = 1000,
-  summary.fx = median, dist.method = "euclidean", subsamples = seq(0,
-  1, by = 0.01), dimensions = ceiling(length(selection) * 0.05),
-  metaMDS.opts = list(), threads = 2, verbosity = 1, points,
-  pre.tribs)
-}
-\arguments{
-\item{dist}{Distances as a \code{dist} object.}
-
-\item{selection}{Objects to include in the subsample. By default, all objects are
-selected.}
-
-\item{replicates}{Number of replications per point.}
-
-\item{summary.fx}{Function to summarize the distance distributions in a given replicate. By
-default, the median distance is estimated.}
-
-\item{dist.method}{Distance method between random points and samples in the transformed
-space. See \code{dist}.}
-
-\item{subsamples}{Subsampling fractions.}
-
-\item{dimensions}{Dimensions to use in the NMDS. By default, 5\% of the selection length.}
-
-\item{metaMDS.opts}{Any additional options to pass to metaMDS, as \code{list}.}
-
-\item{threads}{Number of threads to use.}
-
-\item{verbosity}{Verbosity. Use 0 to run quietly, increase for additional information.}
-
-\item{points}{Optional. If passed, the MDS step is skipped and this object is used
-instead.  It can be the \code{$points} slot of class \code{metaMDS} 
-(from \code{vegan}).
-It must be a matrix or matrix-coercible object, with samples as rows and
-dimensions as columns.}
-
-\item{pre.tribs}{Optional. If passed, the points are recovered from this object (except if
-\code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object 
-estimated on the same objects (the selection is unimportant).}
-}
-\value{
-Returns an \code{\link{enve.TRIBS}} object.
-}
-\description{
-Subsample any objects in "distance space" to reduce the effect of
-sample-clustering. This function was originally designed to subsample
-genomes in "phylogenetic distance space", a clear case of strong
-clustering bias in sampling, by Luis M. Rodriguez-R and Michael R
-Weigand.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd

@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tribs.R
-\name{enve.tribs.test}
-\alias{enve.tribs.test}
-\title{Enveomics: TRIBS Test}
-\usage{
-enve.tribs.test(dist, selection, bins = 50, ...)
-}
-\arguments{
-\item{dist}{Distances as \code{dist} object.}
-
-\item{selection}{Selection defining the subset.}
-
-\item{bins}{Number of bins to evaluate in the range of distances.}
-
-\item{...}{Any other parameters supported by \code{\link{enve.tribs}}, 
-except \code{subsamples}.}
-}
-\value{
-Returns an \code{\link{enve.TRIBStest}} object.
-}
-\description{
-Estimates the empirical difference between all the distances in a set of
-objects and a subset, together with its statistical significance.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}