1. metagenomeSeq
  2. Commit a94b8b09cd1dcc832454a0ea140bf1ba46fc2735
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Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

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Commit id: 13226f5c172a2e5e54a61e521a57d13b5ef50863
Commit message:
Added sl param to aggTax
Committed by nosson <nosson at gmail.com>
Commit date: 2014-02-28T12:16:03-08:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@86937 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 28/02/2014 20:16:15
Showing 3 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
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 Package: metagenomeSeq
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 Title: Statistical analysis for sparse high-throughput sequencing
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-Version: 1.5.40
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-Date: 2013-02-24
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+Version: 1.5.41
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+Date: 2013-02-28
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 Author: Joseph Nathaniel Paulson, Mihai Pop,  Hector Corrada Bravo
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 Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu>
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 Description: metagenomeSeq is designed to determine features (be it Operational
R/aggregateByTaxonomy.R
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@@ -12,6 +12,7 @@
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 #' @param norm Whether to aggregate normalized counts or not.
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 #' @param log Whether or not to log2 transform the counts - if MRexperiment object.
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 #' @param aggfun Aggregation function.
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+#' @param sl scaling value, default is 1000.
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 #' @return An aggregated count matrix.
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 #' @aliases aggTax
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 #' @rdname aggregateByTaxonomy
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@@ -21,9 +22,9 @@
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 #' # not run
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 #' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
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 #'
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-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums){
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+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000){
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 	if(class(obj)=="MRexperiment"){
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-		mat = MRcounts(obj,norm=norm,log=log)
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+		mat = MRcounts(obj,norm=norm,log=log,sl=sl)
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     } else {
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 		stop("Object needs to be a MRexperiment object. If it's a matrix, see aggregateM.")
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     }
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@@ -49,6 +50,6 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun
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 }
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 #' @rdname aggregateByTaxonomy
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 #' @export
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-aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums){
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-    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun)
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+aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000){
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+    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl)
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 }
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\ No newline at end of file
man/aggregateByTaxonomy.Rd
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@@ -9,10 +9,10 @@ to the desired level using the aggfun function (default colSums). Possible aggfu
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 include colMeans and colMedians.}
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 \usage{
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 aggregateByTaxonomy(obj, lvl, alternate = FALSE, norm = TRUE, log = FALSE,
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-  aggfun = colSums)
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+  aggfun = colSums, sl = 1000)
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 aggTax(obj, lvl, alternate = FALSE, norm = TRUE, log = FALSE,
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-  aggfun = colSums)
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+  aggfun = colSums, sl = 1000)
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 }
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 \arguments{
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   \item{obj}{A MRexperiment object.}
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@@ -30,6 +30,8 @@ aggTax(obj, lvl, alternate = FALSE, norm = TRUE, log = FALSE,
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   if MRexperiment object.}
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   \item{aggfun}{Aggregation function.}
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+
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+  \item{sl}{scaling value, default is 1000.}
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 }
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 \value{
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 An aggregated count matrix.