git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84095 bc3139a8-67e5-0310-9ffc-ced21a209358
Joseph Paulson authored on 09/12/2013 23:50:35
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@@ -1,4 +1,5 @@ |
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-#' Aggregates a MRexperiment object by a particular taxonomic level. |
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+#' @name aggregateByTaxonomy |
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+#' @title Aggregates a MRexperiment object by a particular taxonomic level. |
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#' |
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#' Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a |
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#' MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts |
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@@ -10,7 +11,8 @@ |
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#' @param norm Whether to aggregate normalized counts or not. |
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#' @param aggfun Aggregation function. |
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#' @return An aggregated count matrix. |
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-#' @aliases aggregateTax, aggTax |
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+#' @aliases aggTax |
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+#' @rdname aggregateByTaxonomy |
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#' @export |
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#' @examples |
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#' |
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@@ -34,4 +36,9 @@ aggregateByTaxonomy<-function(obj,lvl,norm=TRUE,aggfun = colSums){
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rownames(newMat) = names(grps) |
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colnames(newMat) = sampleNames(obj) |
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newMat |
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+} |
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+#' @rdname aggregateByTaxonomy |
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+#' @export |
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+aggTax<-function(obj,lvl,norm=TRUE,aggfun = colSums){
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+ aggregateByTaxonomy(obj,lvl,norm=TRUE,aggfun = colSums) |
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} |
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\ No newline at end of file |
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@@ -1,10 +1,16 @@ |
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\name{aggregateByTaxonomy}
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\alias{aggTax}
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\alias{aggregateByTaxonomy}
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-\alias{aggregateTax,}
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-\title{Aggregates a MRexperiment object by a particular taxonomic level.}
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+\title{Aggregates a MRexperiment object by a particular taxonomic level.
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+ |
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+Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a |
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+MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts |
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+to the desired level by with the aggfun function (default colSums). Possible aggfun alternatives |
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+include colMeans and colMedians.} |
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\usage{
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aggregateByTaxonomy(obj, lvl, norm = TRUE, aggfun = colSums) |
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+ |
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+aggTax(obj, lvl, norm = TRUE, aggfun = colSums) |
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} |
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\arguments{
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\item{obj}{A MRexperiment object.}
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@@ -21,6 +27,9 @@ aggregateByTaxonomy(obj, lvl, norm = TRUE, aggfun = colSums) |
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An aggregated count matrix. |
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} |
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\description{
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+Aggregates a MRexperiment object by a particular taxonomic |
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+level. |
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+ |
|
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Using the featureData information in the MRexperiment, |
| 25 | 34 |
calling aggregateByTaxonomy on a MRexperiment and a |
| 26 | 35 |
particular featureData column (i.e. 'genus') will aggregate |