[med-svn] [r-bioc-metagenomeseq] 02/06: New upstream version 1.18.0
Andreas Tille
tille at debian.org
Sun Oct 1 15:57:27 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-metagenomeseq.
commit 97840a2769ef41346d3c41e8d4395258652436bb
Author: Andreas Tille <tille at debian.org>
Date: Sun Oct 1 17:35:57 2017 +0200
New upstream version 1.18.0
---
DESCRIPTION | 6 +--
R/aggregateByTaxonomy.R | 105 ++++++++++++++++++++++-----------------
R/fitTimeSeries.R | 60 ++++++++++++++--------
build/vignette.rds | Bin 296 -> 295 bytes
inst/doc/fitTimeSeries.pdf | Bin 241572 -> 242261 bytes
inst/doc/metagenomeSeq.Rnw | 2 +-
inst/doc/metagenomeSeq.pdf | Bin 998018 -> 998910 bytes
man/MRcoefs.Rd | 1 -
man/MRcounts.Rd | 1 -
man/MRexperiment2biom.Rd | 1 -
man/MRfulltable.Rd | 1 -
man/MRtable.Rd | 1 -
man/aggregateBySample.Rd | 4 +-
man/aggregateByTaxonomy.Rd | 14 ++++--
man/biom2MRexperiment.Rd | 1 -
man/calcNormFactors.Rd | 1 -
man/calcPosComponent.Rd | 1 -
man/calcShrinkParameters.Rd | 1 -
man/calcStandardError.Rd | 1 -
man/calcZeroAdjustment.Rd | 1 -
man/calcZeroComponent.Rd | 1 -
man/calculateEffectiveSamples.Rd | 1 -
man/correctIndices.Rd | 1 -
man/correlationTest.Rd | 3 +-
man/cumNorm.Rd | 1 -
man/cumNormMat.Rd | 1 -
man/cumNormStat.Rd | 1 -
man/cumNormStatFast.Rd | 1 -
man/doCountMStep.Rd | 1 -
man/doEStep.Rd | 1 -
man/doZeroMStep.Rd | 1 -
man/expSummary.Rd | 1 -
man/exportMat.Rd | 1 -
man/exportStats.Rd | 1 -
man/extractMR.Rd | 1 -
man/filterData.Rd | 1 -
man/fitDO.Rd | 1 -
man/fitFeatureModel.Rd | 1 -
man/fitLogNormal.Rd | 1 -
man/fitMultipleTimeSeries.Rd | 5 +-
man/fitPA.Rd | 1 -
man/fitSSTimeSeries.Rd | 5 +-
man/fitTimeSeries.Rd | 5 +-
man/fitZeroLogNormal.Rd | 1 -
man/fitZig.Rd | 1 -
man/getCountDensity.Rd | 1 -
man/getEpsilon.Rd | 1 -
man/getNegativeLogLikelihoods.Rd | 1 -
man/getPi.Rd | 1 -
man/getZ.Rd | 1 -
man/isItStillActive.Rd | 1 -
man/libSize-set.Rd | 1 -
man/libSize.Rd | 1 -
man/loadBiom.Rd | 1 -
man/loadMeta.Rd | 1 -
man/loadMetaQ.Rd | 1 -
man/loadPhenoData.Rd | 1 -
man/makeLabels.Rd | 1 -
man/mergeMRexperiments.Rd | 1 -
man/mergeTable.Rd | 1 -
man/metagenomeSeq-deprecated.Rd | 7 ++-
man/newMRexperiment.Rd | 1 -
man/normFactors-set.Rd | 1 -
man/normFactors.Rd | 1 -
man/plotBubble.Rd | 1 -
man/plotClassTimeSeries.Rd | 1 -
man/plotCorr.Rd | 1 -
man/plotFeature.Rd | 1 -
man/plotGenus.Rd | 3 +-
man/plotMRheatmap.Rd | 1 -
man/plotOTU.Rd | 1 -
man/plotOrd.Rd | 1 -
man/plotRare.Rd | 1 -
man/plotTimeSeries.Rd | 1 -
man/posteriorProbs.Rd | 1 -
man/returnAppropriateObj.Rd | 1 -
man/ssFit.Rd | 1 -
man/ssIntervalCandidate.Rd | 1 -
man/ssPerm.Rd | 1 -
man/ssPermAnalysis.Rd | 1 -
man/trapz.Rd | 1 -
man/ts2MRexperiment.Rd | 6 ++-
man/uniqueFeatures.Rd | 1 -
man/zigControl.Rd | 3 +-
vignettes/metagenomeSeq.Rnw | 2 +-
85 files changed, 133 insertions(+), 164 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 3b8cc1b..04377cd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: metagenomeSeq
Title: Statistical analysis for sparse high-throughput sequencing
-Version: 1.16.0
+Version: 1.18.0
Date: 2016-07-21
Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada
Bravo
@@ -24,6 +24,6 @@ biocViews: Classification, Clustering, GeneticVariability,
DifferentialExpression, Microbiome, Metagenomics,
Normalization, Visualization, MultipleComparison, Sequencing,
Software
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
NeedsCompilation: no
-Packaged: 2016-10-17 23:12:48 UTC; biocbuild
+Packaged: 2017-04-24 23:30:36 UTC; biocbuild
diff --git a/R/aggregateByTaxonomy.R b/R/aggregateByTaxonomy.R
index ffc4645..83faf8a 100644
--- a/R/aggregateByTaxonomy.R
+++ b/R/aggregateByTaxonomy.R
@@ -13,6 +13,8 @@
#' @param aggfun Aggregation function.
#' @param sl scaling value, default is 1000.
#' @param out Either 'MRexperiment' or 'matrix'
+#' @param featureOrder Hierarchy of levels in taxonomy as fData colnames
+#' @param returnFullHierarchy Boolean value to indicate return single column of fData or all columns of hierarchy
#' @return An aggregated count matrix.
#' @aliases aggTax
#' @rdname aggregateByTaxonomy
@@ -25,53 +27,64 @@
#' # aggregateByTaxonomy(mouseData,lvl="class",norm=TRUE,aggfun=colMedians)
#' # aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)
#'
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
- if(class(obj)=="MRexperiment"){
- mat = MRcounts(obj,norm=norm,log=log,sl=sl)
- if(length(lvl)==1) levels = as.character(fData(obj)[,lvl])
- else levels = as.character(lvl)
- } else {
- mat = obj
- levels = as.character(lvl)
- if(length(levels)!=nrow(mat)) stop("If input is a count matrix, lvl must be a vector of length = nrow(count matrix)")
- }
- if(!(out%in%c("MRexperiment","matrix"))){
- stop("The variable out must either be 'MRexperiment' or 'matrix'")
- }
-
- nafeatures = is.na(levels)
- if(length(nafeatures)>0){
- if(alternate==FALSE){
- levels[nafeatures] = "no_match"
- } else {
- levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
- }
- }
- grps = split(seq_along(levels),levels)
-
- newMat = array(NA,dim=c(length(grps),ncol(obj)))
- for(i in seq_along(grps)){
- newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
- }
- rownames(newMat) = names(grps)
- colnames(newMat) = colnames(obj)
- if(out=='matrix') return(newMat)
- if(out=='MRexperiment'){
- taxa = data.frame(names(grps))
- colnames(taxa) = "Taxa"
- rownames(taxa) = names(grps)
- taxa = as(taxa,"AnnotatedDataFrame")
- if(class(obj)=="MRexperiment"){
- pd = phenoData(obj)
- newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
- } else {
- newObj = newMRexperiment(newMat,featureData=taxa)
- }
- return(newObj)
- }
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,featureOrder=NULL,returnFullHierarchy=TRUE,out="MRexperiment"){
+ if(class(obj)=="MRexperiment"){
+ mat = MRcounts(obj,norm=norm,log=log,sl=sl)
+ if(length(lvl)==1) levels = as.character(fData(obj)[,lvl])
+ else levels = as.character(lvl)
+ } else {
+ mat = obj
+ levels = as.character(lvl)
+ if(length(levels)!=nrow(mat)) stop("If input is a count matrix, lvl must be a vector of length = nrow(count matrix)")
+ }
+ if(!(out%in%c("MRexperiment","matrix"))){
+ stop("The variable out must either be 'MRexperiment' or 'matrix'")
+ }
+
+ nafeatures = is.na(levels)
+ if(length(nafeatures)>0){
+ if(alternate==FALSE){
+ levels[nafeatures] = "no_match"
+ } else {
+ levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
+ }
+ }
+ grps = split(seq_along(levels),levels)
+
+ newMat = array(NA,dim=c(length(grps),ncol(obj)))
+ for(i in seq_along(grps)){
+ newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
+ }
+ rownames(newMat) = names(grps)
+ colnames(newMat) = colnames(obj)
+ if(out=='matrix') return(newMat)
+ if(out=='MRexperiment'){
+ if(returnFullHierarchy){
+
+ if(is.null(featureOrder)){
+ featureOrder <- colnames(fData(obj))
+ }
+
+ taxa = featureData(obj)[match(names(grps), fData(obj)[,lvl]),featureOrder[1:which(featureOrder == lvl)]]
+ featureNames(taxa) = names(grps)
+ } else{
+ taxa = data.frame(names(grps))
+ colnames(taxa) = "Taxa"
+ rownames(taxa) = names(grps)
+ taxa = as(taxa,"AnnotatedDataFrame")
+ }
+
+ if(class(obj)=="MRexperiment"){
+ pd = phenoData(obj)
+ newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
+ } else {
+ newObj = newMRexperiment(newMat,featureData=taxa)
+ }
+ return(newObj)
+ }
}
#' @rdname aggregateByTaxonomy
#' @export
-aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
- aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
+aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,featureOrder=NULL,returnFullHierarchy=TRUE,out='MRexperiment'){
+ aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,featureOrder=featureOrder,returnFullHierarchy=returnFullHierarchy,out=out)
}
diff --git a/R/fitTimeSeries.R b/R/fitTimeSeries.R
index c3ae47d..a8fb3ec 100644
--- a/R/fitTimeSeries.R
+++ b/R/fitTimeSeries.R
@@ -234,6 +234,7 @@ ssIntervalCandidate <- function(fit, standardError, timePoints, positive=TRUE,C=
#' @param norm When aggregating counts to normalize or not.
#' @param log Log2 transform.
#' @param sl Scaling value.
+#' @param featureOrder Hierarchy of levels in taxonomy as fData colnames
#' @param ... Options for ssanova
#' @return List of matrix of time point intervals of interest, Difference in abundance area and p-value, fit, area permutations, and call.
#' @return A list of objects including:
@@ -253,10 +254,10 @@ ssIntervalCandidate <- function(fit, standardError, timePoints, positive=TRUE,C=
#' res = fitSSTimeSeries(obj=mouseData,feature="Actinobacteria",
#' class="status",id="mouseID",time="relativeTime",lvl='class',B=2)
#'
-fitSSTimeSeries <- function(obj,formula,feature,class,time,id,lvl=NULL,include=c("class", "time:class"),C=0,B=1000,norm=TRUE,log=TRUE,sl=1000,...) {
+fitSSTimeSeries <- function(obj,formula,feature,class,time,id,lvl=NULL,include=c("class", "time:class"),C=0,B=1000,norm=TRUE,log=TRUE,sl=1000,featureOrder=NULL,...) {
if(!is.null(lvl)){
- aggData = aggregateByTaxonomy(obj,lvl,norm=norm,sl=sl)
+ aggData = aggregateByTaxonomy(obj,lvl,norm=norm,sl=sl, featureOrder=featureOrder)
abundance = MRcounts(aggData,norm=FALSE,log=log,sl=1)[feature,]
} else {
abundance = MRcounts(obj,norm=norm,log=log,sl=sl)[feature,]
@@ -347,6 +348,7 @@ fitSSTimeSeries <- function(obj,formula,feature,class,time,id,lvl=NULL,include=c
#' @param norm When aggregating counts to normalize or not.
#' @param log Log2 transform.
#' @param sl Scaling value.
+#' @param featureOrder Hierarchy of levels in taxonomy as fData colnames
#' @param ... Options for ssanova
#' @return List of matrix of time point intervals of interest, Difference in abundance area and p-value, fit, area permutations, and call.
#' @return A list of objects including:
@@ -368,16 +370,16 @@ fitSSTimeSeries <- function(obj,formula,feature,class,time,id,lvl=NULL,include=c
#'
fitTimeSeries <- function(obj,formula,feature,class,time,id,method=c("ssanova"),
lvl=NULL,include=c("class", "time:class"),C=0,B=1000,
- norm=TRUE,log=TRUE,sl=1000,...) {
+ norm=TRUE,log=TRUE,sl=1000,featureOrder=NULL,...) {
if(method=="ssanova"){
if(requireNamespace("gss")){
if(missing(formula)){
res = fitSSTimeSeries(obj=obj,feature=feature,class=class,time=time,id=id,
- lvl=lvl,C=C,B=B,norm=norm,log=log,sl=sl,include=include,...)
+ lvl=lvl,C=C,B=B,norm=norm,log=log,sl=sl,include=include,featureOrder=featureOrder,...)
} else {
res = fitSSTimeSeries(obj=obj,formula=formula,feature=feature,class=class,
time=time,id=id,lvl=lvl,C=C,B=B,norm=norm,log=log,sl=sl,
- include=include,...)
+ include=include,featureOrder=featureOrder,...)
}
}
}
@@ -494,6 +496,7 @@ plotClassTimeSeries<-function(res,formula,xlab="Time",ylab="Abundance",color0="b
#' @param obj metagenomeSeq MRexperiment-class object.
#' @param lvl Vector or name of column in featureData of MRexperiment-class object for aggregating counts (if not OTU level).
#' @param B Number of permutations to perform.
+#' @param featureOrder Hierarchy of levels in taxonomy as fData colnames
#' @param ... Options for \code{\link{fitTimeSeries}}, except feature.
#' @return List of lists of matrices of time point intervals of interest, Difference in abundance area and p-value, fit, area permutations.
#' @return A list of lists for which each includes:
@@ -513,7 +516,7 @@ plotClassTimeSeries<-function(res,formula,xlab="Time",ylab="Abundance",color0="b
#' res = fitMultipleTimeSeries(obj=mouseData,lvl='phylum',class="status",
#' id="mouseID",time="relativeTime",B=1)
#'
-fitMultipleTimeSeries <- function(obj,lvl=NULL,B=1,...) {
+fitMultipleTimeSeries <- function(obj,lvl=NULL,B=1,featureOrder=NULL,...) {
if(is.null(lvl)){
bacteria = seq(nrow(obj))
} else {
@@ -523,7 +526,7 @@ fitMultipleTimeSeries <- function(obj,lvl=NULL,B=1,...) {
bacteria = unique(fData(obj)[,lvl])
}
fits = lapply(bacteria,function(bact){
- try(fitTimeSeries(obj,lvl=lvl,feature=bact,B=B,...))
+ try(fitTimeSeries(obj,lvl=lvl,feature=bact,B=B,featureOrder=featureOrder,...))
})
names(fits) = bacteria
fits = c(fits,call=match.call())
@@ -540,6 +543,7 @@ fitMultipleTimeSeries <- function(obj,lvl=NULL,B=1,...) {
#' @param taxonomyHierarchyRoot Root of feature hierarchy for MRexperiment
#' @param taxonomyDescription Description of features for plot axis label
#' @param featuresOfInterest The features to select from the fitMultipleTimeSeries output
+#' @param featureDataOfInterest featureData for the resulting MRexperiment
#' @return MRexperiment that contains fitTimeSeries data, featureData, and phenoData
#' @rdname ts2MRexperiment
#' @seealso \code{\link{fitTimeSeries}} \code{\link{fitMultipleTimeSeries}}
@@ -557,7 +561,8 @@ ts2MRexperiment<-function(obj,sampleNames=NULL,
taxonomyLevels=NULL,
taxonomyHierarchyRoot="bacteria",
taxonomyDescription="taxonomy",
- featuresOfInterest = NULL){
+ featuresOfInterest = NULL,
+ featureDataOfInterest=NULL){
if(is.null(obj)){
stop("Matrix cannot be null")
}
@@ -567,24 +572,30 @@ ts2MRexperiment<-function(obj,sampleNames=NULL,
}
if(is.null(featuresOfInterest)){
- hasFit <- lapply(1:length(obj), function(i) which(!is.null(obj[[i]]$fit)))
+ hasFit <- lapply(1:(length(obj)-1), function(i) which(!is.null(obj[[i]]$fit)))
featuresOfInterest <- which(hasFit == 1)
+ hasFit <- (hasFit == 1)
+ hasFit <- !is.na(hasFit)
+ temp <- 1:length(hasFit)
+ temp[!hasFit] <- 0
+ hasFit <- temp
}
if(is.null(taxonomyLevels)){
- numLevels <- length(featuresOfInterest)
- taxonomyLevels <- names(obj)[featuresOfInterest]
+ numLevels <- 1:length(hasFit)
+ taxonomyLevels <- names(obj)[1:length(hasFit)]
}
-
+
numSamples <- length(sampleNames)
numLevels <- length(taxonomyLevels)
numFeaturesOfInterest <- length(featuresOfInterest)
-
+
rangeSamples <- 1:numSamples
rangeFeaturesOfInterest <- 1:numFeaturesOfInterest
-
- results <- do.call(rbind, lapply(rangeFeaturesOfInterest,function(i){ t(obj[[featuresOfInterest[i]]]$fit)[1,]}))
-
+# print(hasFit)
+
+ results <- do.call(rbind, lapply(hasFit,function(i){ if (i != 0) t(obj[[i]]$fit)[1,] else rep(NA, numSamples) }))
+
dfSamples <- data.frame(x=rangeSamples,row.names=sampleNames)
metaDataSamples <-data.frame(labelDescription=sampleDescription)
annotatedDFSamples <- AnnotatedDataFrame()
@@ -592,12 +603,17 @@ ts2MRexperiment<-function(obj,sampleNames=NULL,
varMetadata(annotatedDFSamples) <- metaDataSamples
validObject(annotatedDFSamples)
- dfFeatures <- data.frame(taxonomy1=rep(taxonomyHierarchyRoot, numLevels),taxonomy2=taxonomyLevels)
- metaDataFeatures <-data.frame(labelDescription=paste(taxonomyDescription, 1:2, sep=""))
- annotatedDFFeatures <- AnnotatedDataFrame()
- pData(annotatedDFFeatures) <- dfFeatures
- varMetadata(annotatedDFFeatures) <- metaDataFeatures
- validObject(annotatedDFFeatures)
+ if(is.null(featureDataOfInterest)){
+ dfFeatures <- data.frame(taxonomy1=rep(taxonomyHierarchyRoot, numLevels),taxonomy2=taxonomyLevels)
+ metaDataFeatures <-data.frame(labelDescription=paste(taxonomyDescription, 1:2, sep=""))
+ annotatedDFFeatures <- AnnotatedDataFrame()
+ pData(annotatedDFFeatures) <- dfFeatures
+ varMetadata(annotatedDFFeatures) <- metaDataFeatures
+ validObject(annotatedDFFeatures)
+ }
+ else{
+ annotatedDFFeatures <- featureDataOfInterest
+ }
fitTimeSeriesMRexp <- newMRexperiment(counts=results,
phenoData=annotatedDFSamples,
diff --git a/build/vignette.rds b/build/vignette.rds
index 5705571..a1be299 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/fitTimeSeries.pdf b/inst/doc/fitTimeSeries.pdf
index be51fe1..83a0517 100644
Binary files a/inst/doc/fitTimeSeries.pdf and b/inst/doc/fitTimeSeries.pdf differ
diff --git a/inst/doc/metagenomeSeq.Rnw b/inst/doc/metagenomeSeq.Rnw
index 2ded587..4dc45b6 100644
--- a/inst/doc/metagenomeSeq.Rnw
+++ b/inst/doc/metagenomeSeq.Rnw
@@ -306,7 +306,7 @@ system(paste("rm",file.path(dataDirectory,"tmp.tsv")))
\newpage
\section{Statistical testing}
-Now that we have taken care of normalization we can address the effects of under sampling on the detecting differentially abundant features (OTUs, genes, etc). This is our latest development and we recommend \textit{fitFeatureModel} over \textit{fitZig}. \textit{MRcoefs}, \textit{MRtable} and \textit{MRfulltable} are useful summary tables of the model outputs.
+Now that we have taken care of normalization we can address the effects of under sampling on detecting differentially abundant features (OTUs, genes, etc). This is our latest development and we recommend \textit{fitFeatureModel} over \textit{fitZig}. \textit{MRcoefs}, \textit{MRtable} and \textit{MRfulltable} are useful summary tables of the model outputs.
\subsection{Zero-inflated Log-Normal mixture model for each feature}
By reparametrizing our zero-inflation model, we're able to fit a zero-inflated model for each specific OTU separately.
diff --git a/inst/doc/metagenomeSeq.pdf b/inst/doc/metagenomeSeq.pdf
index d3f3442..efbce2a 100644
Binary files a/inst/doc/metagenomeSeq.pdf and b/inst/doc/metagenomeSeq.pdf differ
diff --git a/man/MRcoefs.Rd b/man/MRcoefs.Rd
index 5cd0a16..725ac5c 100644
--- a/man/MRcoefs.Rd
+++ b/man/MRcoefs.Rd
@@ -69,4 +69,3 @@ head(MRcoefs(fit))
\seealso{
\code{\link{fitZig}} \code{\link{fitFeatureModel}} \code{\link{MRtable}} \code{\link{MRfulltable}}
}
-
diff --git a/man/MRcounts.Rd b/man/MRcounts.Rd
index 028cfcd..d587a0c 100644
--- a/man/MRcounts.Rd
+++ b/man/MRcounts.Rd
@@ -34,4 +34,3 @@ head(MRcounts(lungData))
\author{
Joseph N. Paulson, jpaulson at umiacs.umd.edu
}
-
diff --git a/man/MRexperiment2biom.Rd b/man/MRexperiment2biom.Rd
index f538de6..fa9ac33 100644
--- a/man/MRexperiment2biom.Rd
+++ b/man/MRexperiment2biom.Rd
@@ -29,4 +29,3 @@ Wrapper to convert MRexperiment objects to biom objects.
\seealso{
\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}} \code{\link{biom2MRexperiment}}
}
-
diff --git a/man/MRfulltable.Rd b/man/MRfulltable.Rd
index 4cfa883..53aa455 100644
--- a/man/MRfulltable.Rd
+++ b/man/MRfulltable.Rd
@@ -74,4 +74,3 @@ fit = fitFeatureModel(obj = lungTrim,mod=mod)
\code{\link{fitZig}} \code{\link{fitFeatureModel}} \code{\link{MRcoefs}} \code{\link{MRtable}}
\code{\link{fitPA}}
}
-
diff --git a/man/MRtable.Rd b/man/MRtable.Rd
index 9d50411..a03395a 100644
--- a/man/MRtable.Rd
+++ b/man/MRtable.Rd
@@ -72,4 +72,3 @@ head(MRtable(fit))
\seealso{
\code{\link{fitZig}} \code{\link{fitFeatureModel}} \code{\link{MRcoefs}} \code{\link{MRfulltable}}
}
-
diff --git a/man/aggregateBySample.Rd b/man/aggregateBySample.Rd
index 20d219d..10b4062 100644
--- a/man/aggregateBySample.Rd
+++ b/man/aggregateBySample.Rd
@@ -1,8 +1,9 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/aggregateBySample.R
\name{aggregateBySample}
-\alias{aggSamp}
\alias{aggregateBySample}
+\alias{aggSamp}
+\alias{aggSamp}
\title{Aggregates a MRexperiment object or counts matrix to by a factor.}
\usage{
aggregateBySample(obj, fct, aggfun = rowMeans, out = "MRexperiment")
@@ -36,4 +37,3 @@ aggregateBySample(mouseData[1:100,],fct="diet",aggfun=rowSums)
# aggSamp(mouseData,fct='diet',aggfun=rowMaxs)
}
-
diff --git a/man/aggregateByTaxonomy.Rd b/man/aggregateByTaxonomy.Rd
index f958237..4c663e2 100644
--- a/man/aggregateByTaxonomy.Rd
+++ b/man/aggregateByTaxonomy.Rd
@@ -1,15 +1,18 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/aggregateByTaxonomy.R
\name{aggregateByTaxonomy}
-\alias{aggTax}
\alias{aggregateByTaxonomy}
+\alias{aggTax}
+\alias{aggTax}
\title{Aggregates a MRexperiment object or counts matrix to a particular level.}
\usage{
aggregateByTaxonomy(obj, lvl, alternate = FALSE, norm = FALSE,
- log = FALSE, aggfun = colSums, sl = 1000, out = "MRexperiment")
+ log = FALSE, aggfun = colSums, sl = 1000, featureOrder = NULL,
+ returnFullHierarchy = TRUE, out = "MRexperiment")
aggTax(obj, lvl, alternate = FALSE, norm = FALSE, log = FALSE,
- aggfun = colSums, sl = 1000, out = "MRexperiment")
+ aggfun = colSums, sl = 1000, featureOrder = NULL,
+ returnFullHierarchy = TRUE, out = "MRexperiment")
}
\arguments{
\item{obj}{A MRexperiment object or count matrix.}
@@ -26,6 +29,10 @@ aggTax(obj, lvl, alternate = FALSE, norm = FALSE, log = FALSE,
\item{sl}{scaling value, default is 1000.}
+\item{featureOrder}{Hierarchy of levels in taxonomy as fData colnames}
+
+\item{returnFullHierarchy}{Boolean value to indicate return single column of fData or all columns of hierarchy}
+
\item{out}{Either 'MRexperiment' or 'matrix'}
}
\value{
@@ -46,4 +53,3 @@ aggregateByTaxonomy(mouseData[1:100,],lvl="class",norm=TRUE,aggfun=colSums)
# aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)
}
-
diff --git a/man/biom2MRexperiment.Rd b/man/biom2MRexperiment.Rd
index ff9600d..88381db 100644
--- a/man/biom2MRexperiment.Rd
+++ b/man/biom2MRexperiment.Rd
@@ -26,4 +26,3 @@ biom2MRexperiment(x)
\seealso{
\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}}
}
-
diff --git a/man/calcNormFactors.Rd b/man/calcNormFactors.Rd
index 4dbe632..1bb033b 100644
--- a/man/calcNormFactors.Rd
+++ b/man/calcNormFactors.Rd
@@ -26,4 +26,3 @@ head(calcNormFactors(mouseData))
\seealso{
\code{\link{fitZig}} \code{\link{cumNormStatFast}} \code{\link{cumNorm}}
}
-
diff --git a/man/calcPosComponent.Rd b/man/calcPosComponent.Rd
index 8750dba..07b2ac1 100644
--- a/man/calcPosComponent.Rd
+++ b/man/calcPosComponent.Rd
@@ -19,4 +19,3 @@ Fit the positive (log-normal) component
\seealso{
\code{\link{fitZeroLogNormal}} \code{\link{fitFeatureModel}}
}
-
diff --git a/man/calcShrinkParameters.Rd b/man/calcShrinkParameters.Rd
index fe5aed2..492cd41 100644
--- a/man/calcShrinkParameters.Rd
+++ b/man/calcShrinkParameters.Rd
@@ -21,4 +21,3 @@ Calculate the shrunken variances and variance of parameters of interest across f
\seealso{
\code{\link{fitZeroLogNormal}} \code{\link{fitFeatureModel}}
}
-
diff --git a/man/calcStandardError.Rd b/man/calcStandardError.Rd
index e4da0c9..8659ebd 100644
--- a/man/calcStandardError.Rd
+++ b/man/calcStandardError.Rd
@@ -25,4 +25,3 @@ zero-inflated log-normal models for semicontinuous data", ED Mills
\seealso{
\code{\link{fitZeroLogNormal}} \code{\link{fitFeatureModel}}
}
-
diff --git a/man/calcZeroAdjustment.Rd b/man/calcZeroAdjustment.Rd
index fb8dd1e..9198978 100644
--- a/man/calcZeroAdjustment.Rd
+++ b/man/calcZeroAdjustment.Rd
@@ -25,4 +25,3 @@ fold change.
\seealso{
\code{\link{fitZeroLogNormal}} \code{\link{fitFeatureModel}}
}
-
diff --git a/man/calcZeroComponent.Rd b/man/calcZeroComponent.Rd
index 7e2e658..f98f42a 100644
--- a/man/calcZeroComponent.Rd
+++ b/man/calcZeroComponent.Rd
@@ -19,4 +19,3 @@ Fit the zero (logisitic) component
\seealso{
\code{\link{fitZeroLogNormal}} \code{\link{fitFeatureModel}}
}
-
diff --git a/man/calculateEffectiveSamples.Rd b/man/calculateEffectiveSamples.Rd
index 9398662..1689f99 100644
--- a/man/calculateEffectiveSamples.Rd
+++ b/man/calculateEffectiveSamples.Rd
@@ -21,4 +21,3 @@ belongs to the technical distribution.
\seealso{
\code{\link{fitZig}} \code{\link{MRcoefs}} \code{\link{MRfulltable}}
}
-
diff --git a/man/correctIndices.Rd b/man/correctIndices.Rd
index 14e1643..942a864 100644
--- a/man/correctIndices.Rd
+++ b/man/correctIndices.Rd
@@ -33,4 +33,3 @@ table(cormat[1,-1] - cors[1:5,1])
\seealso{
\code{\link{correlationTest}}
}
-
diff --git a/man/correlationTest.Rd b/man/correlationTest.Rd
index e5a604b..3fb553f 100644
--- a/man/correlationTest.Rd
+++ b/man/correlationTest.Rd
@@ -1,8 +1,8 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/correlationTest.R
\name{correlationTest}
-\alias{corTest}
\alias{correlationTest}
+\alias{corTest}
\title{Correlation of each row of a matrix or MRexperiment object}
\usage{
correlationTest(obj, y = NULL, method = "pearson",
@@ -58,4 +58,3 @@ head(cors)
\seealso{
\code{\link{correctIndices}}
}
-
diff --git a/man/cumNorm.Rd b/man/cumNorm.Rd
index 4ba687c..472e1f2 100644
--- a/man/cumNorm.Rd
+++ b/man/cumNorm.Rd
@@ -29,4 +29,3 @@ head(normFactors(mouseData))
\seealso{
\code{\link{fitZig}} \code{\link{cumNormStat}}
}
-
diff --git a/man/cumNormMat.Rd b/man/cumNormMat.Rd
index 8e48230..5b36bad 100644
--- a/man/cumNormMat.Rd
+++ b/man/cumNormMat.Rd
@@ -30,4 +30,3 @@ head(cumNormMat(mouseData))
\seealso{
\code{\link{fitZig}} \code{\link{cumNorm}}
}
-
diff --git a/man/cumNormStat.Rd b/man/cumNormStat.Rd
index 1a2c967..634c8ac 100644
--- a/man/cumNormStat.Rd
+++ b/man/cumNormStat.Rd
@@ -36,4 +36,3 @@ p = round(cumNormStat(mouseData,pFlag=FALSE),digits=2)
\seealso{
\code{\link{fitZig}} \code{\link{cumNorm}} \code{\link{cumNormStatFast}}
}
-
diff --git a/man/cumNormStatFast.Rd b/man/cumNormStatFast.Rd
index 9f9287e..f1e238f 100644
--- a/man/cumNormStatFast.Rd
+++ b/man/cumNormStatFast.Rd
@@ -33,4 +33,3 @@ p = round(cumNormStatFast(mouseData,pFlag=FALSE),digits=2)
\seealso{
\code{\link{fitZig}} \code{\link{cumNorm}} \code{\link{cumNormStat}}
}
-
diff --git a/man/doCountMStep.Rd b/man/doCountMStep.Rd
index 941d28f..8969df8 100644
--- a/man/doCountMStep.Rd
+++ b/man/doCountMStep.Rd
@@ -42,4 +42,3 @@ as $z_ij = pr(delta_ij=1 | data)$.
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/doEStep.Rd b/man/doEStep.Rd
index 93bccc2..2538cf9 100644
--- a/man/doEStep.Rd
+++ b/man/doEStep.Rd
@@ -34,4 +34,3 @@ as $z_ij = pr(delta_ij=1 | data)$.
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/doZeroMStep.Rd b/man/doZeroMStep.Rd
index c187527..a5e7d12 100644
--- a/man/doZeroMStep.Rd
+++ b/man/doZeroMStep.Rd
@@ -35,4 +35,3 @@ f_count(y;mu_i,sigma_i^2 )+delta_ij log pi_j(s_j)+(1-delta_ij)log (1-pi_j
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/expSummary.Rd b/man/expSummary.Rd
index 61b1469..2ef1918 100644
--- a/man/expSummary.Rd
+++ b/man/expSummary.Rd
@@ -28,4 +28,3 @@ expSummary(mouseData)
\author{
Joseph N. Paulson, jpaulson at umiacs.umd.edu
}
-
diff --git a/man/exportMat.Rd b/man/exportMat.Rd
index be8eed0..5ce04ba 100644
--- a/man/exportMat.Rd
+++ b/man/exportMat.Rd
@@ -37,4 +37,3 @@ head(read.csv(file=file.path(dataDirectory,"tmp.tsv"),sep="\\t"))
\seealso{
\code{\link{cumNorm}}
}
-
diff --git a/man/exportStats.Rd b/man/exportStats.Rd
index 2a130a1..85e2769 100644
--- a/man/exportStats.Rd
+++ b/man/exportStats.Rd
@@ -32,4 +32,3 @@ head(read.csv(file=file.path(dataDirectory,"tmp.tsv"),sep="\\t"))
\seealso{
\code{\link{cumNorm}} \code{\link{quantile}}
}
-
diff --git a/man/extractMR.Rd b/man/extractMR.Rd
index 734e9be..76122ea 100644
--- a/man/extractMR.Rd
+++ b/man/extractMR.Rd
@@ -27,4 +27,3 @@ data(mouseData)
head(metagenomeSeq:::extractMR(mouseData))
}
-
diff --git a/man/filterData.Rd b/man/filterData.Rd
index dd5eddb..836a44e 100644
--- a/man/filterData.Rd
+++ b/man/filterData.Rd
@@ -26,4 +26,3 @@ data(mouseData)
filterData(mouseData)
}
-
diff --git a/man/fitDO.Rd b/man/fitDO.Rd
index 43f0004..7bba79d 100644
--- a/man/fitDO.Rd
+++ b/man/fitDO.Rd
@@ -48,4 +48,3 @@ head(res)
\seealso{
\code{\link{cumNorm}} \code{\link{fitZig}} \code{\link{fitPA}} \code{\link{fitMeta}}
}
-
diff --git a/man/fitFeatureModel.Rd b/man/fitFeatureModel.Rd
index 362c50b..51252c6 100644
--- a/man/fitFeatureModel.Rd
+++ b/man/fitFeatureModel.Rd
@@ -50,4 +50,3 @@ lungres1 = fitFeatureModel(lungData,mod)
\seealso{
\code{\link{cumNorm}}
}
-
diff --git a/man/fitLogNormal.Rd b/man/fitLogNormal.Rd
index 4c422bf..089abb5 100644
--- a/man/fitLogNormal.Rd
+++ b/man/fitLogNormal.Rd
@@ -43,4 +43,3 @@ mod = model.matrix(~smokingStatus)
fit = fitLogNormal(obj = lungTrim,mod=mod,B=1)
}
-
diff --git a/man/fitMultipleTimeSeries.Rd b/man/fitMultipleTimeSeries.Rd
index 79a19a2..145157c 100644
--- a/man/fitMultipleTimeSeries.Rd
+++ b/man/fitMultipleTimeSeries.Rd
@@ -4,7 +4,7 @@
\alias{fitMultipleTimeSeries}
\title{Discover differentially abundant time intervals for all bacteria}
\usage{
-fitMultipleTimeSeries(obj, lvl = NULL, B = 1, ...)
+fitMultipleTimeSeries(obj, lvl = NULL, B = 1, featureOrder = NULL, ...)
}
\arguments{
\item{obj}{metagenomeSeq MRexperiment-class object.}
@@ -13,6 +13,8 @@ fitMultipleTimeSeries(obj, lvl = NULL, B = 1, ...)
\item{B}{Number of permutations to perform.}
+\item{featureOrder}{Hierarchy of levels in taxonomy as fData colnames}
+
\item{...}{Options for \code{\link{fitTimeSeries}}, except feature.}
}
\value{
@@ -42,4 +44,3 @@ res = fitMultipleTimeSeries(obj=mouseData,lvl='phylum',class="status",
\seealso{
\code{\link{cumNorm}} \code{\link{fitSSTimeSeries}} \code{\link{fitTimeSeries}}
}
-
diff --git a/man/fitPA.Rd b/man/fitPA.Rd
index 28dde21..0e5bf78 100644
--- a/man/fitPA.Rd
+++ b/man/fitPA.Rd
@@ -42,4 +42,3 @@ head(res)
\seealso{
\code{\link{cumNorm}} \code{\link{fitZig}} \code{\link{fitDO}} \code{\link{fitMeta}}
}
-
diff --git a/man/fitSSTimeSeries.Rd b/man/fitSSTimeSeries.Rd
index 8292fd0..0e68237 100644
--- a/man/fitSSTimeSeries.Rd
+++ b/man/fitSSTimeSeries.Rd
@@ -6,7 +6,7 @@
\usage{
fitSSTimeSeries(obj, formula, feature, class, time, id, lvl = NULL,
include = c("class", "time:class"), C = 0, B = 1000, norm = TRUE,
- log = TRUE, sl = 1000, ...)
+ log = TRUE, sl = 1000, featureOrder = NULL, ...)
}
\arguments{
\item{obj}{metagenomeSeq MRexperiment-class object.}
@@ -35,6 +35,8 @@ fitSSTimeSeries(obj, formula, feature, class, time, id, lvl = NULL,
\item{sl}{Scaling value.}
+\item{featureOrder}{Hierarchy of levels in taxonomy as fData colnames}
+
\item{...}{Options for ssanova}
}
\value{
@@ -70,4 +72,3 @@ res = fitSSTimeSeries(obj=mouseData,feature="Actinobacteria",
\seealso{
\code{\link{cumNorm}} \code{\link{ssFit}} \code{\link{ssIntervalCandidate}} \code{\link{ssPerm}} \code{\link{ssPermAnalysis}} \code{\link{plotTimeSeries}}
}
-
diff --git a/man/fitTimeSeries.Rd b/man/fitTimeSeries.Rd
index c2d8f35..83b9313 100644
--- a/man/fitTimeSeries.Rd
+++ b/man/fitTimeSeries.Rd
@@ -6,7 +6,7 @@
\usage{
fitTimeSeries(obj, formula, feature, class, time, id, method = c("ssanova"),
lvl = NULL, include = c("class", "time:class"), C = 0, B = 1000,
- norm = TRUE, log = TRUE, sl = 1000, ...)
+ norm = TRUE, log = TRUE, sl = 1000, featureOrder = NULL, ...)
}
\arguments{
\item{obj}{metagenomeSeq MRexperiment-class object.}
@@ -37,6 +37,8 @@ fitTimeSeries(obj, formula, feature, class, time, id, method = c("ssanova"),
\item{sl}{Scaling value.}
+\item{featureOrder}{Hierarchy of levels in taxonomy as fData colnames}
+
\item{...}{Options for ssanova}
}
\value{
@@ -65,4 +67,3 @@ res = fitTimeSeries(obj=mouseData,feature="Actinobacteria",
\seealso{
\code{\link{cumNorm}} \code{\link{fitSSTimeSeries}} \code{\link{plotTimeSeries}}
}
-
diff --git a/man/fitZeroLogNormal.Rd b/man/fitZeroLogNormal.Rd
index cdb03e4..3968e70 100644
--- a/man/fitZeroLogNormal.Rd
+++ b/man/fitZeroLogNormal.Rd
@@ -40,4 +40,3 @@ and model matrix. Not for the average user, assumes structure of the model matri
\seealso{
\code{\link{cumNorm}} \code{\link{fitFeatureModel}}
}
-
diff --git a/man/fitZig.Rd b/man/fitZig.Rd
index 3e965b4..01559da 100644
--- a/man/fitZig.Rd
+++ b/man/fitZig.Rd
@@ -72,4 +72,3 @@ fit = fitZig(obj = lungTrim,mod=mod,control=settings)
\seealso{
\code{\link{cumNorm}} \code{\link{zigControl}}
}
-
diff --git a/man/getCountDensity.Rd b/man/getCountDensity.Rd
index 6d26a07..fb59dda 100644
--- a/man/getCountDensity.Rd
+++ b/man/getCountDensity.Rd
@@ -29,4 +29,3 @@ f_count(y;mu_i,sigma_i^2 )+delta_ij log pi_j(s_j)+(1-delta_ij)log (1-pi_j
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/getEpsilon.Rd b/man/getEpsilon.Rd
index 86b93ff..4603dbe 100644
--- a/man/getEpsilon.Rd
+++ b/man/getEpsilon.Rd
@@ -28,4 +28,3 @@ as $z_ij = pr(delta_ij=1 | data)$.
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/getNegativeLogLikelihoods.Rd b/man/getNegativeLogLikelihoods.Rd
index 01159fb..4ad5b61 100644
--- a/man/getNegativeLogLikelihoods.Rd
+++ b/man/getNegativeLogLikelihoods.Rd
@@ -30,4 +30,3 @@ as $z_ij = pr(delta_ij=1 | data and current values)$.
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/getPi.Rd b/man/getPi.Rd
index 0402a73..50ca381 100644
--- a/man/getPi.Rd
+++ b/man/getPi.Rd
@@ -23,4 +23,3 @@ from the zero model.
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/getZ.Rd b/man/getZ.Rd
index 4b1aca2..3726f8e 100644
--- a/man/getZ.Rd
+++ b/man/getZ.Rd
@@ -30,4 +30,3 @@ Calculate the current Z estimate responsibilities (posterior probabilities)
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/isItStillActive.Rd b/man/isItStillActive.Rd
index 787bc95..1df7cd8 100644
--- a/man/isItStillActive.Rd
+++ b/man/isItStillActive.Rd
@@ -27,4 +27,3 @@ whether or not the feature's negative log-likelihood (measure of the fit) has ch
\seealso{
\code{\link{fitZig}}
}
-
diff --git a/man/libSize-set.Rd b/man/libSize-set.Rd
index 23e2e87..2cdd202 100644
--- a/man/libSize-set.Rd
+++ b/man/libSize-set.Rd
@@ -29,4 +29,3 @@ head(libSize(lungData)<- rnorm(1))
\author{
Joseph N. Paulson
}
-
diff --git a/man/libSize.Rd b/man/libSize.Rd
index f88ae8d..99f664a 100644
--- a/man/libSize.Rd
+++ b/man/libSize.Rd
@@ -27,4 +27,3 @@ head(libSize(lungData))
\author{
Joseph N. Paulson
}
-
diff --git a/man/loadBiom.Rd b/man/loadBiom.Rd
index dc0ca46..f19bfa8 100644
--- a/man/loadBiom.Rd
+++ b/man/loadBiom.Rd
@@ -25,4 +25,3 @@ x
\seealso{
\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}
}
-
diff --git a/man/loadMeta.Rd b/man/loadMeta.Rd
index 6a61b23..106bd24 100644
--- a/man/loadMeta.Rd
+++ b/man/loadMeta.Rd
@@ -27,4 +27,3 @@ lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))
\seealso{
\code{\link{loadPhenoData}}
}
-
diff --git a/man/loadMetaQ.Rd b/man/loadMetaQ.Rd
index 8869e95..1c297cd 100644
--- a/man/loadMetaQ.Rd
+++ b/man/loadMetaQ.Rd
@@ -24,4 +24,3 @@ Load a matrix of OTUs in Qiime's format
\seealso{
\code{\link{loadMeta}} \code{\link{loadPhenoData}}
}
-
diff --git a/man/loadPhenoData.Rd b/man/loadPhenoData.Rd
index ddfa8cc..503527d 100644
--- a/man/loadPhenoData.Rd
+++ b/man/loadPhenoData.Rd
@@ -30,4 +30,3 @@ clin = loadPhenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)
\seealso{
\code{\link{loadMeta}}
}
-
diff --git a/man/makeLabels.Rd b/man/makeLabels.Rd
index 322bbc6..18d4dfa 100644
--- a/man/makeLabels.Rd
+++ b/man/makeLabels.Rd
@@ -24,4 +24,3 @@ Beginning to transition to better axes for plots
\examples{
metagenomeSeq::makeLabels(norm=TRUE,log=TRUE)
}
-
diff --git a/man/mergeMRexperiments.Rd b/man/mergeMRexperiments.Rd
index 8dd56bf..a6dd6bb 100644
--- a/man/mergeMRexperiments.Rd
+++ b/man/mergeMRexperiments.Rd
@@ -29,4 +29,3 @@ data(lungData)
newobj = mergeMRexperiments(mouseData,lungData)
newobj
}
-
diff --git a/man/mergeTable.Rd b/man/mergeTable.Rd
index d852ad6..d4cc4a4 100644
--- a/man/mergeTable.Rd
+++ b/man/mergeTable.Rd
@@ -17,4 +17,3 @@ Merged table
\description{
Merge two tables
}
-
diff --git a/man/metagenomeSeq-deprecated.Rd b/man/metagenomeSeq-deprecated.Rd
index 273b45c..b2c39f0 100644
--- a/man/metagenomeSeq-deprecated.Rd
+++ b/man/metagenomeSeq-deprecated.Rd
@@ -2,13 +2,13 @@
% Please edit documentation in R/deprecated_metagenomeSeq_function.R
\docType{package}
\name{metagenomeSeq-deprecated}
+\alias{metagenomeSeq-deprecated}
\alias{deprecated_metagenomeSeq_function}
\alias{fitMeta}
-\alias{load_biom}
+\alias{load_phenoData}
\alias{load_meta}
+\alias{load_biom}
\alias{load_metaQ}
-\alias{load_phenoData}
-\alias{metagenomeSeq-deprecated}
\alias{metagenomeSeq-deprecated-package}
\title{Depcrecated functions in the metagenomeSeq package.}
\usage{
@@ -27,4 +27,3 @@ parameters to be passed to the modern version of the function (see table).}
\description{
These functions may be removed completely in the next release.
}
-
diff --git a/man/newMRexperiment.Rd b/man/newMRexperiment.Rd
index f9982e4..5b7f4b7 100644
--- a/man/newMRexperiment.Rd
+++ b/man/newMRexperiment.Rd
@@ -43,4 +43,3 @@ obj <- newMRexperiment(cnts)
\author{
Joseph N Paulson
}
-
diff --git a/man/normFactors-set.Rd b/man/normFactors-set.Rd
index 5018601..dd7aeb4 100644
--- a/man/normFactors-set.Rd
+++ b/man/normFactors-set.Rd
@@ -29,4 +29,3 @@ head(normFactors(lungData)<- rnorm(1))
\author{
Joseph N. Paulson
}
-
diff --git a/man/normFactors.Rd b/man/normFactors.Rd
index 1214d3c..ae80673 100644
--- a/man/normFactors.Rd
+++ b/man/normFactors.Rd
@@ -26,4 +26,3 @@ head(normFactors(lungData))
\author{
Joseph N. Paulson
}
-
diff --git a/man/plotBubble.Rd b/man/plotBubble.Rd
index 4a02ddd..a25341e 100644
--- a/man/plotBubble.Rd
+++ b/man/plotBubble.Rd
@@ -52,4 +52,3 @@ plotBubble(y,x)
\seealso{
\code{\link{plotMRheatmap}}
}
-
diff --git a/man/plotClassTimeSeries.Rd b/man/plotClassTimeSeries.Rd
index cc59e4a..550e54e 100644
--- a/man/plotClassTimeSeries.Rd
+++ b/man/plotClassTimeSeries.Rd
@@ -43,4 +43,3 @@ plotClassTimeSeries(res,pch=21,bg=res$data$class,ylim=c(0,8))
\seealso{
\code{\link{fitTimeSeries}}
}
-
diff --git a/man/plotCorr.Rd b/man/plotCorr.Rd
index 7c210e6..3344074 100644
--- a/man/plotCorr.Rd
+++ b/man/plotCorr.Rd
@@ -37,4 +37,3 @@ plotCorr(obj=mouseData,n=200,cexRow = 0.4,cexCol = 0.4,trace="none",dendrogram="
\seealso{
\code{\link{cumNormMat}}
}
-
diff --git a/man/plotFeature.Rd b/man/plotFeature.Rd
index 0643e3c..ae116f5 100644
--- a/man/plotFeature.Rd
+++ b/man/plotFeature.Rd
@@ -51,4 +51,3 @@ col=dates,sortby=dates,ylab="Raw reads")
\seealso{
\code{\link{cumNorm}}
}
-
diff --git a/man/plotGenus.Rd b/man/plotGenus.Rd
index 88b155a..bc45977 100644
--- a/man/plotGenus.Rd
+++ b/man/plotGenus.Rd
@@ -1,8 +1,8 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotGenus.R
\name{plotGenus}
-\alias{genusPlot}
\alias{plotGenus}
+\alias{genusPlot}
\title{Basic plot function of the raw or normalized data.}
\usage{
plotGenus(obj, otuIndex, classIndex, norm = TRUE, log = TRUE,
@@ -57,4 +57,3 @@ plotGenus(mouseData,otuIndex,classIndex,no=1:2,xaxt="n",norm=FALSE,ylab="Strep n
\seealso{
\code{\link{cumNorm}}
}
-
diff --git a/man/plotMRheatmap.Rd b/man/plotMRheatmap.Rd
index a17f0c7..8e03809 100644
--- a/man/plotMRheatmap.Rd
+++ b/man/plotMRheatmap.Rd
@@ -43,4 +43,3 @@ plotMRheatmap(obj=mouseData,n=50,fun=mad,cexRow = 0.4,cexCol = 0.4,trace="none",
\seealso{
\code{\link{cumNormMat}}
}
-
diff --git a/man/plotOTU.Rd b/man/plotOTU.Rd
index c622766..5550595 100644
--- a/man/plotOTU.Rd
+++ b/man/plotOTU.Rd
@@ -52,4 +52,3 @@ plotOTU(mouseData,otu=9083,classIndex,norm=FALSE,main="9083 feature abundances")
\seealso{
\code{\link{cumNorm}}
}
-
diff --git a/man/plotOrd.Rd b/man/plotOrd.Rd
index 7a966c2..1950431 100644
--- a/man/plotOrd.Rd
+++ b/man/plotOrd.Rd
@@ -48,4 +48,3 @@ plotOrd(mouseData,tran=TRUE,useDist=TRUE,pch=21,bg=factor(cl),usePCA=FALSE)
\seealso{
\code{\link{cumNormMat}}
}
-
diff --git a/man/plotRare.Rd b/man/plotRare.Rd
index ed8f34a..94c117e 100644
--- a/man/plotRare.Rd
+++ b/man/plotRare.Rd
@@ -34,4 +34,3 @@ legend("topleft", c("Diet 1","Diet 2"), text.col=c(1,2),box.col=NA)
\seealso{
\code{\link{plotOrd}}, \code{\link{plotMRheatmap}}, \code{\link{plotCorr}}, \code{\link{plotOTU}}, \code{\link{plotGenus}}
}
-
diff --git a/man/plotTimeSeries.Rd b/man/plotTimeSeries.Rd
index a569c4b..2b27a5d 100644
--- a/man/plotTimeSeries.Rd
+++ b/man/plotTimeSeries.Rd
@@ -38,4 +38,3 @@ plotTimeSeries(res)
\seealso{
\code{\link{fitTimeSeries}}
}
-
diff --git a/man/posteriorProbs.Rd b/man/posteriorProbs.Rd
index 17916bd..72afe1a 100644
--- a/man/posteriorProbs.Rd
+++ b/man/posteriorProbs.Rd
@@ -38,4 +38,3 @@ head(posteriorProbs(lungTrim))
\author{
Joseph N. Paulson
}
-
diff --git a/man/returnAppropriateObj.Rd b/man/returnAppropriateObj.Rd
index 8356612..184f16b 100644
--- a/man/returnAppropriateObj.Rd
+++ b/man/returnAppropriateObj.Rd
@@ -28,4 +28,3 @@ data(lungData)
head(returnAppropriateObj(lungData,norm=FALSE,log=FALSE))
}
-
diff --git a/man/ssFit.Rd b/man/ssFit.Rd
index 36774c5..35051ec 100644
--- a/man/ssFit.Rd
+++ b/man/ssFit.Rd
@@ -45,4 +45,3 @@ the fitted values for the fitted model.
\seealso{
\code{\link{cumNorm}} \code{\link{fitTimeSeries}} \code{\link{ssPermAnalysis}} \code{\link{ssPerm}} \code{\link{ssIntervalCandidate}}
}
-
diff --git a/man/ssIntervalCandidate.Rd b/man/ssIntervalCandidate.Rd
index 373489d..9cfdc75 100644
--- a/man/ssIntervalCandidate.Rd
+++ b/man/ssIntervalCandidate.Rd
@@ -31,4 +31,3 @@ Calculates time intervals of interest using SS-Anova fitted confidence intervals
\seealso{
\code{\link{cumNorm}} \code{\link{fitTimeSeries}} \code{\link{ssFit}} \code{\link{ssPerm}} \code{\link{ssPermAnalysis}}
}
-
diff --git a/man/ssPerm.Rd b/man/ssPerm.Rd
index fa860a3..8bf89ad 100644
--- a/man/ssPerm.Rd
+++ b/man/ssPerm.Rd
@@ -25,4 +25,3 @@ Creates a list of permuted class memberships for the time series permuation test
\seealso{
\code{\link{cumNorm}} \code{\link{fitTimeSeries}} \code{\link{ssFit}} \code{\link{ssPermAnalysis}} \code{\link{ssIntervalCandidate}}
}
-
diff --git a/man/ssPermAnalysis.Rd b/man/ssPermAnalysis.Rd
index c121dee..d626a32 100644
--- a/man/ssPermAnalysis.Rd
+++ b/man/ssPermAnalysis.Rd
@@ -38,4 +38,3 @@ intervals of differential abundance.
\seealso{
\code{\link{cumNorm}} \code{\link{fitTimeSeries}} \code{\link{ssFit}} \code{\link{ssPerm}} \code{\link{ssIntervalCandidate}}
}
-
diff --git a/man/trapz.Rd b/man/trapz.Rd
index 6321731..704d354 100644
--- a/man/trapz.Rd
+++ b/man/trapz.Rd
@@ -34,4 +34,3 @@ Function comes from the pracma package.
trapz(x, y) - h^2/12 * (cb - ca) #=> 1.999999969
}
-
diff --git a/man/ts2MRexperiment.Rd b/man/ts2MRexperiment.Rd
index f97eeae..7e653fd 100644
--- a/man/ts2MRexperiment.Rd
+++ b/man/ts2MRexperiment.Rd
@@ -7,7 +7,8 @@ an MRexperiment that can be plotted with metavizr}
\usage{
ts2MRexperiment(obj, sampleNames = NULL, sampleDescription = "timepoints",
taxonomyLevels = NULL, taxonomyHierarchyRoot = "bacteria",
- taxonomyDescription = "taxonomy", featuresOfInterest = NULL)
+ taxonomyDescription = "taxonomy", featuresOfInterest = NULL,
+ featureDataOfInterest = NULL)
}
\arguments{
\item{obj}{Output of fitMultipleTimeSeries}
@@ -23,6 +24,8 @@ ts2MRexperiment(obj, sampleNames = NULL, sampleDescription = "timepoints",
\item{taxonomyDescription}{Description of features for plot axis label}
\item{featuresOfInterest}{The features to select from the fitMultipleTimeSeries output}
+
+\item{featureDataOfInterest}{featureData for the resulting MRexperiment}
}
\value{
MRexperiment that contains fitTimeSeries data, featureData, and phenoData
@@ -43,4 +46,3 @@ obj
\seealso{
\code{\link{fitTimeSeries}} \code{\link{fitMultipleTimeSeries}}
}
-
diff --git a/man/uniqueFeatures.Rd b/man/uniqueFeatures.Rd
index 1b93f3f..906af41 100644
--- a/man/uniqueFeatures.Rd
+++ b/man/uniqueFeatures.Rd
@@ -28,4 +28,3 @@ data(mouseData)
head(uniqueFeatures(mouseData[1:100,],cl=pData(mouseData)[,3]))
}
-
diff --git a/man/zigControl.Rd b/man/zigControl.Rd
index 944958e..09489c3 100644
--- a/man/zigControl.Rd
+++ b/man/zigControl.Rd
@@ -1,8 +1,8 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/zigControl.R
\name{zigControl}
-\alias{settings2}
\alias{zigControl}
+\alias{settings2}
\title{Settings for the fitZig function}
\usage{
zigControl(tol = 1e-04, maxit = 10, verbose = TRUE,
@@ -35,4 +35,3 @@ control = zigControl(tol=1e-10,maxit=10,verbose=FALSE)
\seealso{
\code{\link{fitZig}} \code{\link{cumNorm}} \code{\link{plotOTU}}
}
-
diff --git a/vignettes/metagenomeSeq.Rnw b/vignettes/metagenomeSeq.Rnw
index 2ded587..4dc45b6 100644
--- a/vignettes/metagenomeSeq.Rnw
+++ b/vignettes/metagenomeSeq.Rnw
@@ -306,7 +306,7 @@ system(paste("rm",file.path(dataDirectory,"tmp.tsv")))
\newpage
\section{Statistical testing}
-Now that we have taken care of normalization we can address the effects of under sampling on the detecting differentially abundant features (OTUs, genes, etc). This is our latest development and we recommend \textit{fitFeatureModel} over \textit{fitZig}. \textit{MRcoefs}, \textit{MRtable} and \textit{MRfulltable} are useful summary tables of the model outputs.
+Now that we have taken care of normalization we can address the effects of under sampling on detecting differentially abundant features (OTUs, genes, etc). This is our latest development and we recommend \textit{fitFeatureModel} over \textit{fitZig}. \textit{MRcoefs}, \textit{MRtable} and \textit{MRfulltable} are useful summary tables of the model outputs.
\subsection{Zero-inflated Log-Normal mixture model for each feature}
By reparametrizing our zero-inflation model, we're able to fit a zero-inflated model for each specific OTU separately.
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-metagenomeseq.git
More information about the debian-med-commit
mailing list