Update documentation

hms-dbmi · Oct 8, 2015 · d054b7c · d054b7c
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diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,3 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
-
 export(bwpca)
 export(knn.error.models)
 export(make.pagoda.app)

diff --git a/man/ViewPagodaApp-class.Rd b/man/ViewPagodaApp-class.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \docType{class}
 \name{ViewPagodaApp-class}

diff --git a/man/bwpca.Rd b/man/bwpca.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{bwpca}
 \alias{bwpca}

diff --git a/man/es.mef.small.Rd b/man/es.mef.small.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \docType{data}
 \name{es.mef.small}

diff --git a/man/knn.Rd b/man/knn.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \docType{data}
 \name{knn}

diff --git a/man/knn.error.models.Rd b/man/knn.error.models.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{knn.error.models}
 \alias{knn.error.models}

diff --git a/man/make.pagoda.app.Rd b/man/make.pagoda.app.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{make.pagoda.app}
 \alias{make.pagoda.app}

diff --git a/man/o.ifm.Rd b/man/o.ifm.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \docType{data}
 \name{o.ifm}

diff --git a/man/pagoda.cluster.cells.Rd b/man/pagoda.cluster.cells.Rd
@@ -1,18 +1,18 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.cluster.cells}
 \alias{pagoda.cluster.cells}
 \title{Determine optimal cell clustering based on the genes driving the significant aspects}
 \usage{
-pagoda.cluster.cells(tam, varinfo, method = "ward", include.aspects = FALSE,
-  verbose = 0, return.details = FALSE)
+pagoda.cluster.cells(tam, varinfo, method = "ward.D",
+  include.aspects = FALSE, verbose = 0, return.details = FALSE)
 }
 \arguments{
 \item{tam}{result of pagoda.top.aspects() call}
 
 \item{varinfo}{result of pagoda.varnorm() call}
 
-\item{method}{clustering method ('ward' by default)}
+\item{method}{clustering method ('ward.D' by default)}
 
 \item{include.aspects}{whether the aspect patterns themselves should be included alongside with the individual genes in calculating cell distance}
 

diff --git a/man/pagoda.effective.cells.Rd b/man/pagoda.effective.cells.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.effective.cells}
 \alias{pagoda.effective.cells}

diff --git a/man/pagoda.gene.clusters.Rd b/man/pagoda.gene.clusters.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.gene.clusters}
 \alias{pagoda.gene.clusters}
@@ -8,7 +8,7 @@ pagoda.gene.clusters(varinfo, trim = 3.1/ncol(varinfo$mat),
   n.clusters = 150, n.samples = 60, cor.method = "p",
   n.internal.shuffles = 0, n.starts = 10, n.cores = detectCores(),
   verbose = 0, plot = FALSE, show.random = FALSE, n.components = 1,
-  method = "ward", secondary.correlation = FALSE,
+  method = "ward.D", secondary.correlation = FALSE,
   n.cells = ncol(varinfo$mat), old.results = NULL)
 }
 \arguments{

diff --git a/man/pagoda.pathway.wPCA.Rd b/man/pagoda.pathway.wPCA.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.pathway.wPCA}
 \alias{pagoda.pathway.wPCA}

diff --git a/man/pagoda.reduce.loading.redundancy.Rd b/man/pagoda.reduce.loading.redundancy.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.reduce.loading.redundancy}
 \alias{pagoda.reduce.loading.redundancy}

diff --git a/man/pagoda.reduce.redundancy.Rd b/man/pagoda.reduce.redundancy.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.reduce.redundancy}
 \alias{pagoda.reduce.redundancy}

diff --git a/man/pagoda.show.pathways.Rd b/man/pagoda.show.pathways.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.show.pathways}
 \alias{pagoda.show.pathways}

diff --git a/man/pagoda.subtract.aspect.Rd b/man/pagoda.subtract.aspect.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.subtract.aspect}
 \alias{pagoda.subtract.aspect}

diff --git a/man/pagoda.top.aspects.Rd b/man/pagoda.top.aspects.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.top.aspects}
 \alias{pagoda.top.aspects}

diff --git a/man/pagoda.varnorm.Rd b/man/pagoda.varnorm.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.varnorm}
 \alias{pagoda.varnorm}

diff --git a/man/pagoda.view.aspects.Rd b/man/pagoda.view.aspects.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{pagoda.view.aspects}
 \alias{pagoda.view.aspects}

diff --git a/man/papply.Rd b/man/papply.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/functions.R
+\name{papply}
+\alias{papply}
+\title{wrapper around different mclapply mechanisms}
+\usage{
+papply(..., n.cores = n)
+}
+\arguments{
+\item{...}{parameters to pass to lapply, mclapply, bplapply, etc.}
+
+\item{n.cores}{number of cores. If 1 core is requested, will default to lapply}
+}
+\description{
+Abstracts out mclapply implementation, and defaults to lapply when only one core is requested (helps with debugging)
+}
+
diff --git a/man/pollen.Rd b/man/pollen.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \docType{data}
 \name{pollen}

diff --git a/man/scde.Rd b/man/scde.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \docType{package}
 \name{scde}

diff --git a/man/scde.browse.diffexp.Rd b/man/scde.browse.diffexp.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.browse.diffexp}
 \alias{scde.browse.diffexp}

diff --git a/man/scde.error.models.Rd b/man/scde.error.models.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.error.models}
 \alias{scde.error.models}
@@ -9,7 +9,7 @@ scde.error.models(counts, groups = NULL, min.nonfailed = 3,
   zero.count.threshold = min.count.threshold, zero.lambda = 0.1,
   save.crossfit.plots = FALSE, save.model.plots = TRUE, n.cores = 12,
   min.size.entries = 2000, max.pairs = 5000, min.pairs.per.cell = 10,
-  verbose = 0, linear.fit = TRUE, local.theta.fit = TRUE,
+  verbose = 0, linear.fit = TRUE, local.theta.fit = linear.fit,
   theta.fit.range = c(0.01, 100))
 }
 \arguments{
@@ -41,9 +41,9 @@ scde.error.models(counts, groups = NULL, min.nonfailed = 3,
 
 \item{verbose}{1 for increased output}
 
-\item{linear.fit}{Boolean of whether to use a linear fit in the regression (default: TRUE)}
+\item{linear.fit}{Boolean of whether to use a linear fit in the regression (default: TRUE).}
 
-\item{local.theta.fit}{Boolean of whether to fit the overdispersion parameter theta, ie. the negative binomial size parameter, based on local regression (default: TRUE)}
+\item{local.theta.fit}{Boolean of whether to fit the overdispersion parameter theta, ie. the negative binomial size parameter, based on local regression (default: set to be equal to the linear.fit parameter)}
 
 \item{theta.fit.range}{Range of valid values for the overdispersion parameter theta, ie. the negative binomial size parameter (default: c(1e-2, 1e2))}
 }
@@ -53,6 +53,9 @@ a model matrix, with rows corresponding to different cells, and columns represen
 \description{
 Fit error models given a set of single-cell data (counts) and an optional grouping factor (groups). The cells (within each group) are first cross-compared to determine a subset of genes showing consistent expression. The set of genes is then used to fit a mixture model (Poisson-NB mixture, with expression-dependent concomitant).
 }
+\details{
+Note: the default implementation has been changed to use linear-scale fit with expression-dependent NB size (overdispersion) fit. This represents an interative improvement on the originally published model. Use linear.fit=F to revert back to the original fitting procedure.
+}
 \examples{
 \donttest{
 data(es.mef.small)

diff --git a/man/scde.expression.difference.Rd b/man/scde.expression.difference.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.expression.difference}
 \alias{scde.expression.difference}

diff --git a/man/scde.expression.magnitude.Rd b/man/scde.expression.magnitude.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.expression.magnitude}
 \alias{scde.expression.magnitude}

diff --git a/man/scde.expression.prior.Rd b/man/scde.expression.prior.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.expression.prior}
 \alias{scde.expression.prior}

diff --git a/man/scde.failure.probability.Rd b/man/scde.failure.probability.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.failure.probability}
 \alias{scde.failure.probability}

diff --git a/man/scde.fit.models.to.reference.Rd b/man/scde.fit.models.to.reference.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.fit.models.to.reference}
 \alias{scde.fit.models.to.reference}

diff --git a/man/scde.posteriors.Rd b/man/scde.posteriors.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.posteriors}
 \alias{scde.posteriors}

diff --git a/man/scde.test.gene.expression.difference.Rd b/man/scde.test.gene.expression.difference.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{scde.test.gene.expression.difference}
 \alias{scde.test.gene.expression.difference}

diff --git a/man/show.app.Rd b/man/show.app.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{show.app}
 \alias{show.app}

diff --git a/man/view.aspects.Rd b/man/view.aspects.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{view.aspects}
 \alias{view.aspects}

diff --git a/man/winsorize.matrix.Rd b/man/winsorize.matrix.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/functions.R
 \name{winsorize.matrix}
 \alias{winsorize.matrix}