1. metagenomeSeq
  2. R
  3. aggregateByTaxonomy.R
Browse code

Fixing documentation, fixing case of variable names, adding default return option for taxonomy

From: Justin Wagner <jmwagner@umd.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@128606 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 12/04/2017 16:20:10
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ bb82536
... ... 
@@ -13,6 +13,8 @@
13 13 
 #' @param aggfun Aggregation function.
14 14 
 #' @param sl scaling value, default is 1000.
15 15 
 #' @param out Either 'MRexperiment' or 'matrix'
16 
+#' @param featureOrder Hierarchy of levels in taxonomy as fData colnames
17 
+#' @param returnFullHierarchy Boolean value to indicate return single column of fData or all columns of hierarchy
16 18 
 #' @return An aggregated count matrix.
17 19 
 #' @aliases aggTax
18 20 
 #' @rdname aggregateByTaxonomy
... ... 
@@ -25,7 +27,7 @@
25 27 
 #' # aggregateByTaxonomy(mouseData,lvl="class",norm=TRUE,aggfun=colMedians)
26 28 
 #' # aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)
27 29 
 #'
28 
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,feature_order=NULL,out="MRexperiment"){
30 
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,featureOrder=NULL,returnFullHierarchy=TRUE,out="MRexperiment"){
29 31 
   if(class(obj)=="MRexperiment"){
30 32 
     mat = MRcounts(obj,norm=norm,log=log,sl=sl)
31 33 
     if(length(lvl)==1) levels = as.character(fData(obj)[,lvl])
... ... 
@@ -57,13 +59,21 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
57 59 
   colnames(newMat) = colnames(obj)
58 60 
   if(out=='matrix') return(newMat)
59 61 
   if(out=='MRexperiment'){
60 
-    if(is.null(feature_order)){
61 
-      feature_order <- colnames(fData(obj))
62 
+    if(returnFullHierarchy){
63 
+
64 
+      if(is.null(featureOrder)){
65 
+        featureOrder <- colnames(fData(obj))
66 
+      }
67 
+
68 
+      taxa = featureData(obj)[match(names(grps), fData(obj)[,lvl]),featureOrder[1:which(featureOrder == lvl)]]
69 
+      featureNames(taxa) = names(grps)
70 
+    } else{
71 
+       taxa = data.frame(names(grps))
72 
+       colnames(taxa) = "Taxa"
73 
+       rownames(taxa) = names(grps)
74 
+       taxa = as(taxa,"AnnotatedDataFrame")
62 75 
     }
63 
-
64 
-    taxa = featureData(obj)[match(names(grps), fData(obj)[,lvl]),feature_order[1:which(feature_order == lvl)]]
65 
-    featureNames(taxa) = names(grps)
66 
-
76 
+
67 77 
     if(class(obj)=="MRexperiment"){
68 78 
       pd = phenoData(obj)
69 79 
       newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
... ... 
@@ -75,6 +85,6 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
75 85 
 }
76 86 
 #' @rdname aggregateByTaxonomy
77 87 
 #' @export
78 
-aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
79 
-	aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
88 
+aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,featureOrder=NULL,returnFullHierarchy=TRUE,out='MRexperiment'){
89 
+  aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,featureOrder=featureOrder,returnFullHierarchy=returnFullHierarchy,out=out)
80 90 
 }
Browse code

Making aggregate by taxonomy return full hierarchy tree and connecting to fitTimeSeries aggregate calls

From: Justin Wagner <jmwagner@umd.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@128146 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 06/04/2017 17:27:14
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 5505bd1
... ... 
@@ -25,50 +25,53 @@
25 25 
 #' # aggregateByTaxonomy(mouseData,lvl="class",norm=TRUE,aggfun=colMedians)
26 26 
 #' # aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)
27 27 
 #'
28 
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
29 
-	if(class(obj)=="MRexperiment"){
30 
-		mat = MRcounts(obj,norm=norm,log=log,sl=sl)
31 
-		if(length(lvl)==1) levels = as.character(fData(obj)[,lvl])
32 
-		else levels = as.character(lvl)
33 
-	} else {
34 
-		mat = obj
35 
-		levels = as.character(lvl)
36 
-		if(length(levels)!=nrow(mat)) stop("If input is a count matrix, lvl must be a vector of length = nrow(count matrix)")
37 
-	}
38 
-	if(!(out%in%c("MRexperiment","matrix"))){
39 
-		stop("The variable out must either be 'MRexperiment' or 'matrix'")
40 
-	}
41 
-
42 
-	nafeatures = is.na(levels)
43 
-	if(length(nafeatures)>0){
44 
-		if(alternate==FALSE){
45 
-			levels[nafeatures] = "no_match"
46 
-		} else {
47 
-			levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
48 
-		}
49 
-	}
50 
-	grps = split(seq_along(levels),levels)
51 
-
52 
-	newMat = array(NA,dim=c(length(grps),ncol(obj)))
53 
-	for(i in seq_along(grps)){
54 
-		newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
55 
-	}
56 
-	rownames(newMat) = names(grps)
57 
-	colnames(newMat) = colnames(obj)
58 
-	if(out=='matrix') return(newMat)
59 
-	if(out=='MRexperiment'){
60 
-		taxa = data.frame(names(grps))
61 
-		colnames(taxa) = "Taxa"
62 
-		rownames(taxa) = names(grps)
63 
-		taxa = as(taxa,"AnnotatedDataFrame")
64 
-		if(class(obj)=="MRexperiment"){
65 
-			pd = phenoData(obj)
66 
-			newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
67 
-		} else {
68 
-			newObj = newMRexperiment(newMat,featureData=taxa)
69 
-		}
70 
-		return(newObj)
71 
-	}
28 
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,feature_order=NULL,out="MRexperiment"){
29 
+  if(class(obj)=="MRexperiment"){
30 
+    mat = MRcounts(obj,norm=norm,log=log,sl=sl)
31 
+    if(length(lvl)==1) levels = as.character(fData(obj)[,lvl])
32 
+    else levels = as.character(lvl)
33 
+  } else {
34 
+    mat = obj
35 
+    levels = as.character(lvl)
36 
+    if(length(levels)!=nrow(mat)) stop("If input is a count matrix, lvl must be a vector of length = nrow(count matrix)")
37 
+  }
38 
+  if(!(out%in%c("MRexperiment","matrix"))){
39 
+    stop("The variable out must either be 'MRexperiment' or 'matrix'")
40 
+  }
41 
+
42 
+  nafeatures = is.na(levels)
43 
+  if(length(nafeatures)>0){
44 
+    if(alternate==FALSE){
45 
+      levels[nafeatures] = "no_match"
46 
+    } else {
47 
+      levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
48 
+    }
49 
+  }
50 
+  grps = split(seq_along(levels),levels)
51 
+
52 
+  newMat = array(NA,dim=c(length(grps),ncol(obj)))
53 
+  for(i in seq_along(grps)){
54 
+    newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
55 
+  }
56 
+  rownames(newMat) = names(grps)
57 
+  colnames(newMat) = colnames(obj)
58 
+  if(out=='matrix') return(newMat)
59 
+  if(out=='MRexperiment'){
60 
+    if(is.null(feature_order)){
61 
+      feature_order <- colnames(fData(obj))
62 
+    }
63 
+
64 
+    taxa = featureData(obj)[match(names(grps), fData(obj)[,lvl]),feature_order[1:which(feature_order == lvl)]]
65 
+    featureNames(taxa) = names(grps)
66 
+
67 
+    if(class(obj)=="MRexperiment"){
68 
+      pd = phenoData(obj)
69 
+      newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
70 
+    } else {
71 
+      newObj = newMRexperiment(newMat,featureData=taxa)
72 
+    }
73 
+    return(newObj)
74 
+  }
72 75 
 }
73 76 
 #' @rdname aggregateByTaxonomy
74 77 
 #' @export
Browse code

updated man pages

From: jnpaulson <nosson@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@116423 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 17/04/2016 20:15:24
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ fdfd989
... ... 
@@ -1,7 +1,6 @@
1 
-#' @name aggregateByTaxonomy
2 
-#' @title Aggregates a MRexperiment object or counts matrix to a particular level.
1 
+#' Aggregates a MRexperiment object or counts matrix to a particular level.
3 2 
 #'
4 
-#' @details Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a
3 
+#' Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a
5 4 
 #' MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts
6 5 
 #' to the desired level using the aggfun function (default colSums). Possible aggfun alternatives
7 6 
 #' include colMeans and colMedians.
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d2ab43afc28741e4da5b868a82bb26162bd55ced

many minor tweaks



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@100579 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/03/2015 02:20:42
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 46a0152
... ... 
@@ -63,7 +63,7 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
63 63 
 		rownames(taxa) = names(grps)
64 64 
 		taxa = as(taxa,"AnnotatedDataFrame")
65 65 
 		if(class(obj)=="MRexperiment"){
66 
-			pd = as(pData(obj),"AnnotatedDataFrame")
66 
+			pd = phenoData(obj)
67 67 
 			newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
68 68 
 		} else {
69 69 
 			newObj = newMRexperiment(newMat,featureData=taxa)
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 5ad5ee28cc745947cf2a79d89658082efe22a3c5

fixing hector's comments

Committed by: nosson
Author Name: nosson
Commit date: 2015-01-21 17:53:50 -0500
Author date: 2015-01-21 17:53:50 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@98565 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 21/01/2015 22:54:04
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 49754a9
... ... 
@@ -51,7 +51,7 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
51 51 
 	grps = split(seq_along(levels),levels)
52 52
53 53 
 	newMat = array(NA,dim=c(length(grps),ncol(obj)))
54 
-	for(i in 1:length(grps)){
54 
+	for(i in seq_along(grps)){
55 55 
 		newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
56 56 
 	}
57 57 
 	rownames(newMat) = names(grps)
... ... 
@@ -76,69 +76,3 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
76 76 
 aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
77 77 
 	aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
78 78 
 }
79 
-
80 
-#' @name aggregateBySample
81 
-#' @title Aggregates a MRexperiment object or counts matrix to by a factor.
82 
-#'
83 
-#' @details Using the phenoData information in the MRexperiment, calling aggregateBySample on a
84 
-#' MRexperiment and a particular phenoData column (i.e. 'diet') will aggregate counts
85 
-#' using the aggfun function (default rowMeans). Possible aggfun alternatives
86 
-#' include rowMeans and rowMedians.
87 
-#'
88 
-#' @param obj A MRexperiment object or count matrix.
89 
-#' @param fct phenoData column name from the MRexperiment object or if count matrix object a vector of labels.
90 
-#' @param aggfun Aggregation function.
91 
-#' @param out Either 'MRexperiment' or 'matrix'
92 
-#' @return An aggregated count matrix or MRexperiment object.
93 
-#' @aliases aggSamp
94 
-#' @rdname aggregateBySample
95 
-#' @export
96 
-#' @examples
97 
-#'
98 
-#' data(mouseData)
99 
-#' aggregateBySample(mouseData[1:100,],fct="diet",aggfun=rowSums)
100 
-#' # not run
101 
-#' # aggregateBySample(mouseData,fct="diet",aggfun=rowMedians)
102 
-#' # aggSamp(mouseData,fct='diet',aggfun=rowMaxs)
103 
-#'
104 
-aggregateBySample<-function(obj,fct,aggfun=rowMeans,out="MRexperiment"){
105 
-	if(class(obj)=="MRexperiment"){
106 
-		mat = MRcounts(obj)
107 
-		if(length(fct)==1) factors = as.character(pData(obj)[,fct])
108 
-		else factors = as.character(fct)
109 
-	} else {
110 
-		mat = obj
111 
-		factors = as.character(fct)
112 
-		if(length(factors)!=ncol(mat)) stop("If input is a count matrix, fct must be a vector of length = ncol(count matrix)")
113 
-	}
114 
-	if(!(out%in%c("MRexperiment","matrix"))){
115 
-		stop("The variable out must either be 'MRexperiment' or 'matrix'")
116 
-	}
117 
-	grps = split(seq_along(factors),factors)
118 
-
119 
-	newMat = array(NA,dim=c(nrow(obj),length(grps)))
120 
-	for(i in 1:length(grps)){
121 
-		newMat[,i] = aggfun(mat[,grps[[i]],drop=FALSE])
122 
-	}
123 
-	colnames(newMat) = names(grps)
124 
-	rownames(newMat) = rownames(obj)
125 
-	if(out=='matrix') return(newMat)
126 
-	if(out=='MRexperiment'){
127 
-		pd = data.frame(names(grps))
128 
-		colnames(pd) = "pd"
129 
-		rownames(pd) = names(grps)
130 
-		pd = as(pd,"AnnotatedDataFrame")
131 
-		if(class(obj)=="MRexperiment"){
132 
-			fd = as(fData(obj),"AnnotatedDataFrame")
133 
-			newObj = newMRexperiment(newMat,featureData=fd,phenoData=pd)
134 
-		} else {
135 
-			newObj = newMRexperiment(newMat,phenoData=pd)
136 
-		}
137 
-		return(newObj)
138 
-	}
139 
-}
140 
-#' @rdname aggregateBySample
141 
-#' @export
142 
-aggSamp<-function(obj,fct,aggfun=rowMeans,out='MRexperiment'){
143 
-	aggregateBySample(obj,fct,aggfun=aggfun,out=out)
144 
-}
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 384d1491ac0ebcb21e634d8274ab1974244270bd

adding aggregateBySample

Committed by: nosson
Author Name: nosson
Commit date: 2015-01-21 01:15:42 -0500
Author date: 2015-01-21 01:15:42 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@98545 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 21/01/2015 06:15:51
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 4144cba
... ... 
@@ -76,3 +76,69 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
76 76 
 aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
77 77 
 	aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
78 78 
 }
79 
+
80 
+#' @name aggregateBySample
81 
+#' @title Aggregates a MRexperiment object or counts matrix to by a factor.
82 
+#'
83 
+#' @details Using the phenoData information in the MRexperiment, calling aggregateBySample on a
84 
+#' MRexperiment and a particular phenoData column (i.e. 'diet') will aggregate counts
85 
+#' using the aggfun function (default rowMeans). Possible aggfun alternatives
86 
+#' include rowMeans and rowMedians.
87 
+#'
88 
+#' @param obj A MRexperiment object or count matrix.
89 
+#' @param fct phenoData column name from the MRexperiment object or if count matrix object a vector of labels.
90 
+#' @param aggfun Aggregation function.
91 
+#' @param out Either 'MRexperiment' or 'matrix'
92 
+#' @return An aggregated count matrix or MRexperiment object.
93 
+#' @aliases aggSamp
94 
+#' @rdname aggregateBySample
95 
+#' @export
96 
+#' @examples
97 
+#'
98 
+#' data(mouseData)
99 
+#' aggregateBySample(mouseData[1:100,],fct="diet",aggfun=rowSums)
100 
+#' # not run
101 
+#' # aggregateBySample(mouseData,fct="diet",aggfun=rowMedians)
102 
+#' # aggSamp(mouseData,fct='diet',aggfun=rowMaxs)
103 
+#'
104 
+aggregateBySample<-function(obj,fct,aggfun=rowMeans,out="MRexperiment"){
105 
+	if(class(obj)=="MRexperiment"){
106 
+		mat = MRcounts(obj)
107 
+		if(length(fct)==1) factors = as.character(pData(obj)[,fct])
108 
+		else factors = as.character(fct)
109 
+	} else {
110 
+		mat = obj
111 
+		factors = as.character(fct)
112 
+		if(length(factors)!=ncol(mat)) stop("If input is a count matrix, fct must be a vector of length = ncol(count matrix)")
113 
+	}
114 
+	if(!(out%in%c("MRexperiment","matrix"))){
115 
+		stop("The variable out must either be 'MRexperiment' or 'matrix'")
116 
+	}
117 
+	grps = split(seq_along(factors),factors)
118 
+
119 
+	newMat = array(NA,dim=c(nrow(obj),length(grps)))
120 
+	for(i in 1:length(grps)){
121 
+		newMat[,i] = aggfun(mat[,grps[[i]],drop=FALSE])
122 
+	}
123 
+	colnames(newMat) = names(grps)
124 
+	rownames(newMat) = rownames(obj)
125 
+	if(out=='matrix') return(newMat)
126 
+	if(out=='MRexperiment'){
127 
+		pd = data.frame(names(grps))
128 
+		colnames(pd) = "pd"
129 
+		rownames(pd) = names(grps)
130 
+		pd = as(pd,"AnnotatedDataFrame")
131 
+		if(class(obj)=="MRexperiment"){
132 
+			fd = as(fData(obj),"AnnotatedDataFrame")
133 
+			newObj = newMRexperiment(newMat,featureData=fd,phenoData=pd)
134 
+		} else {
135 
+			newObj = newMRexperiment(newMat,phenoData=pd)
136 
+		}
137 
+		return(newObj)
138 
+	}
139 
+}
140 
+#' @rdname aggregateBySample
141 
+#' @export
142 
+aggSamp<-function(obj,fct,aggfun=rowMeans,out='MRexperiment'){
143 
+	aggregateBySample(obj,fct,aggfun=aggfun,out=out)
144 
+}
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Commit information:

Commit id: 6aad92462d6f6957c071b5105680fb4426cab3a9

updating man pages/R functions adding modified degrees of freedom

Committed by: nosson
Author Name: nosson
Commit date: 2014-11-29 15:49:59 -0500
Author date: 2014-11-29 15:49:59 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@97223 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 29/11/2014 20:50:14
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ dd097c7
... ... 
@@ -20,8 +20,10 @@
20 20 
 #' @export
21 21 
 #' @examples
22 22 
 #'
23 
+#' data(mouseData)
24 
+#' aggregateByTaxonomy(mouseData[1:100,],lvl="class",norm=TRUE,aggfun=colSums)
23 25 
 #' # not run
24 
-#' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
26 
+#' # aggregateByTaxonomy(mouseData,lvl="class",norm=TRUE,aggfun=colMedians)
25 27 
 #' # aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)
26 28 
 #'
27 29 
 aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
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Commit made by the Bioconductor Git-SVN bridge. Consists of 14 commits.

Commit information:

Commit id: bd56b3467846f55b07019b3365efac5dac59123b
Commit message: Merge pull request #11 from nosson/timeseries
Time series method added
Committed by: Joseph N. Paulson
Author Name: Joseph N. Paulson
Commit date: 2014-07-10 16:32:44 -0400
Author date: 2014-07-10 16:32:44 -0400

Commit id: 9ee0799a0e4c8c4d7f8dfadacbfe507495e81301
Commit message: time-series multiple methods
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 16:30:00 -0400
Author date: 2014-07-10 16:30:00 -0400

Commit id: 03f4cc9f4aa9b187e04e154b2bc1fc2c1c138c85
Commit message: Adding plotTimeSeries in vignette
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 13:06:56 -0400
Author date: 2014-07-10 13:06:56 -0400

Commit id: 869b6ab60e92aa21eb4337cc42d490c469b2e155
Commit message: predict on second class + no interval fix
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:58:54 -0400
Author date: 2014-07-10 12:58:54 -0400

Commit id: 621f52347cbd252186fcda26783311b3d938ee02
Commit message: Fixed no interval errors
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:33:32 -0400
Author date: 2014-07-10 12:33:32 -0400

Commit id: 9822bd6bad1a6492b6fe8e452bd7a42cdb41355c
Commit message: Merge branch 'timeseries' of https://github.com/nosson/metagenomeSeq into timeseries
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:21:22 -0400
Author date: 2014-07-10 12:21:22 -0400

Commit id: 8ddc0a0ad6f5b2337446886a4bddfeba392abe38
Commit message: Squashed commit of the following:
commit 4854dd14140e5c4635cefddc9c7afccb1ac1fadf
Author: Umiacs <nosson@gmail.com>
Date: Thu Jul 10 12:18:51 2014 -0400

updating rd, adding plotTimeSeries and fixing fitTimeSeries abs

commit b002aeda586e2ef3dca8abe535edfbc2e0af8da0
Author: unknown <nosson@gmail.com>
Date: Wed Jul 9 10:38:48 2014 -0400

Adding vignette + seealso in

commit 6fc0766ceadc28e43032e8f4a47c08e6b6d66157
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 16:21:38 2014 -0400

Updating NEWS

commit c7542026ca588b0117effac1a577d7a0d92a29ec
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 16:19:29 2014 -0400

Updating man pages

commit 92e5e345a2eef4e9d51592c392f3270ea9c5b681
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 16:04:22 2014 -0400

Fixed build issues due to time series changes

commit 1a1c071a46239a8d7f8d1a468d633b3e4fa91528
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 15:43:32 2014 -0400

Fixing citation

commit 219a263363260d67bb153a4745d05e4cb5fe378a
Author: nosson <nosson@gmail.com>
Date: Mon Jul 7 15:41:06 2014 -0400

Adding ss-anova functions
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:20:57 -0400
Author date: 2014-07-10 12:20:57 -0400

Commit id: 4854dd14140e5c4635cefddc9c7afccb1ac1fadf
Commit message: updating rd, adding plotTimeSeries and fixing fitTimeSeries abs
Committed by: Umiacs
Author Name: Umiacs
Commit date: 2014-07-10 12:18:51 -0400
Author date: 2014-07-10 12:18:51 -0400

Commit id: b002aeda586e2ef3dca8abe535edfbc2e0af8da0
Commit message: Adding vignette + seealso in
Committed by: unknown
Author Name: unknown
Commit date: 2014-07-09 10:38:48 -0400
Author date: 2014-07-09 10:38:48 -0400

Commit id: 6fc0766ceadc28e43032e8f4a47c08e6b6d66157
Commit message: Updating NEWS
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 16:21:38 -0400
Author date: 2014-07-07 16:21:38 -0400

Commit id: c7542026ca588b0117effac1a577d7a0d92a29ec
Commit message: Updating man pages
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 16:19:29 -0400
Author date: 2014-07-07 16:19:29 -0400

Commit id: 92e5e345a2eef4e9d51592c392f3270ea9c5b681
Commit message: Fixed build issues due to time series changes
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 16:04:22 -0400
Author date: 2014-07-07 16:04:22 -0400

Commit id: 1a1c071a46239a8d7f8d1a468d633b3e4fa91528
Commit message: Fixing citation
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 15:43:32 -0400
Author date: 2014-07-07 15:43:32 -0400

Commit id: 219a263363260d67bb153a4745d05e4cb5fe378a
Commit message: Adding ss-anova functions
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-07 15:41:06 -0400
Author date: 2014-07-07 15:41:06 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@92401 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 10/07/2014 20:36:34
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ e093bc6
... ... 
@@ -1,7 +1,7 @@
1 1 
 #' @name aggregateByTaxonomy
2 2 
 #' @title Aggregates a MRexperiment object or counts matrix to a particular level.
3 3 
 #'
4 
-#' Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a
4 
+#' @details Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a
5 5 
 #' MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts
6 6 
 #' to the desired level using the aggfun function (default colSums). Possible aggfun alternatives
7 7 
 #' include colMeans and colMedians.
... ... 
@@ -73,4 +73,4 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
73 73 
 #' @export
74 74 
 aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
75 75 
 	aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
76 
-}
77 76 
\ No newline at end of file
77 
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 47218497f29051f3811d821f86b3e16ff2c1a544
Commit message: aggTax tweak
Committed by: nosson
Author Name: nosson
Commit date: 2014-07-01 01:16:40 -0400
Author date: 2014-07-01 01:16:40 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@92045 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 01/07/2014 05:16:52
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ f12f833
... ... 
@@ -27,7 +27,8 @@
27 27 
 aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
28 28 
 	if(class(obj)=="MRexperiment"){
29 29 
 		mat = MRcounts(obj,norm=norm,log=log,sl=sl)
30 
-		levels = as.character(fData(obj)[,lvl])
30 
+		if(length(lvl)==1) levels = as.character(fData(obj)[,lvl])
31 
+		else levels = as.character(lvl)
31 32 
 	} else {
32 33 
 		mat = obj
33 34 
 		levels = as.character(lvl)
... ... 
@@ -65,8 +66,6 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfu
65 66 
 		} else {
66 67 
 			newObj = newMRexperiment(newMat,featureData=taxa)
67 68 
 		}
68 
-		warning("\n\nThe output here are aggregated counts.\n
69 
-			Check default parameters for all metagenomeSeq functions and consider normalization.")
70 69 
 		return(newObj)
71 70 
 	}
72 71 
 }
Browse code

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

Commit information:

Commit id: eb4c389c4d932922d89f34321e58c9aa74f72e14
Commit message:
Updating aggregateByTaxonomy and defaults for the fun.
Committed by nosson <nosson at gmail.com>
Commit date: 2014-03-09T23:17:57-04:00

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@87245 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 10/03/2014 03:18:09
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ bb840b9
... ... 
@@ -1,5 +1,5 @@
1 1 
 #' @name aggregateByTaxonomy
2 
-#' @title Aggregates a MRexperiment object by a particular taxonomic level.
2 
+#' @title Aggregates a MRexperiment object or counts matrix to a particular level.
3 3 
 #'
4 4 
 #' Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a
5 5 
 #' MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts
... ... 
@@ -22,8 +22,9 @@
22 22 
 #'
23 23 
 #' # not run
24 24 
 #' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
25 
+#' # aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)
25 26 
 #'
26 
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
27 
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
27 28 
 	if(class(obj)=="MRexperiment"){
28 29 
 		mat = MRcounts(obj,norm=norm,log=log,sl=sl)
29 30 
 		levels = as.character(fData(obj)[,lvl])
... ... 
@@ -64,13 +65,13 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun
64 65 
 		} else {
65 66 
 			newObj = newMRexperiment(newMat,featureData=taxa)
66 67 
 		}
67 
-		warning("\n\nThe output here are aggregated (normalized?) counts.\n
68 
-			Check default parameters for all metagenomeSeq functions so as not to renormalize.")
68 
+		warning("\n\nThe output here are aggregated counts.\n
69 
+			Check default parameters for all metagenomeSeq functions and consider normalization.")
69 70 
 		return(newObj)
70 71 
 	}
71 72 
 }
72 73 
 #' @rdname aggregateByTaxonomy
73 74 
 #' @export
74 
-aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
75 
+aggTax<-function(obj,lvl,alternate=FALSE,norm=FALSE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
75 76 
 	aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
76 77 
 }
77 78 
\ No newline at end of file
Browse code

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

Commit information:

Commit id: 03e4c65352e9ec7e037d948d0741e50891ea0604
Commit message:
Making aggregateByTaxonomy/aggTax more versatile
Committed by nosson <nosson at gmail.com>
Commit date: 2014-03-09T22:55:44-04:00

Commit id: f61b99590946fdcf9b7c0e7c38f9b6276a288f9a
Commit message:
Merge branch 'master' of https://github.com/nosson/metagenomeSeq
Committed by nosson <nosson at gmail.com>
Commit date: 2014-03-09T22:55:48-04:00

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@87243 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 10/03/2014 02:56:00
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 3479237
... ... 
@@ -6,13 +6,14 @@
6 6 
 #' to the desired level using the aggfun function (default colSums). Possible aggfun alternatives
7 7 
 #' include colMeans and colMedians.
8 8 
 #'
9 
-#' @param obj A MRexperiment object.
10 
-#' @param lvl featureData column name from the MRexperiment object.
9 
+#' @param obj A MRexperiment object or count matrix.
10 
+#' @param lvl featureData column name from the MRexperiment object or if count matrix object a vector of labels.
11 11 
 #' @param alternate Use the rowname for undefined OTUs instead of aggregating to "no_match".
12 12 
 #' @param norm Whether to aggregate normalized counts or not.
13 13 
 #' @param log Whether or not to log2 transform the counts - if MRexperiment object.
14 14 
 #' @param aggfun Aggregation function.
15 15 
 #' @param sl scaling value, default is 1000.
16 
+#' @param out Either 'MRexperiment' or 'matrix'
16 17 
 #' @return An aggregated count matrix.
17 18 
 #' @aliases aggTax
18 19 
 #' @rdname aggregateByTaxonomy
... ... 
@@ -22,22 +23,27 @@
22 23 
 #' # not run
23 24 
 #' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
24 25 
 #'
25 
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000){
26 
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000,out="MRexperiment"){
26 27 
 	if(class(obj)=="MRexperiment"){
27 28 
 		mat = MRcounts(obj,norm=norm,log=log,sl=sl)
28 
-    } else {
29 
-		stop("Object needs to be a MRexperiment object. If it's a matrix, see aggregateM.")
30 
-    }
31 
-
32 
-	levels = as.character(fData(obj)[,lvl])
33 
-    nafeatures = is.na(levels)
34 
-    if(length(nafeatures)>0){
35 
-        if(alternate==FALSE){
36 
-            levels[nafeatures] = "no_match"
37 
-        } else {
38 
-            levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
39 
-        }
40 
-    }
29 
+		levels = as.character(fData(obj)[,lvl])
30 
+	} else {
31 
+		mat = obj
32 
+		levels = as.character(lvl)
33 
+		if(length(levels)!=nrow(mat)) stop("If input is a count matrix, lvl must be a vector of length = nrow(count matrix)")
34 
+	}
35 
+	if(!(out%in%c("MRexperiment","matrix"))){
36 
+		stop("The variable out must either be 'MRexperiment' or 'matrix'")
37 
+	}
38 
+
39 
+	nafeatures = is.na(levels)
40 
+	if(length(nafeatures)>0){
41 
+		if(alternate==FALSE){
42 
+			levels[nafeatures] = "no_match"
43 
+		} else {
44 
+			levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
45 
+		}
46 
+	}
41 47 
 	grps = split(seq_along(levels),levels)
42 48
43 49 
 	newMat = array(NA,dim=c(length(grps),ncol(obj)))
... ... 
@@ -45,11 +51,26 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun
45 51 
 		newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
46 52 
 	}
47 53 
 	rownames(newMat) = names(grps)
48 
-	colnames(newMat) = sampleNames(obj)
49 
-	newMat
54 
+	colnames(newMat) = colnames(obj)
55 
+	if(out=='matrix') return(newMat)
56 
+	if(out=='MRexperiment'){
57 
+		taxa = data.frame(names(grps))
58 
+		colnames(taxa) = "Taxa"
59 
+		rownames(taxa) = names(grps)
60 
+		taxa = as(taxa,"AnnotatedDataFrame")
61 
+		if(class(obj)=="MRexperiment"){
62 
+			pd = as(pData(obj),"AnnotatedDataFrame")
63 
+			newObj = newMRexperiment(newMat,featureData=taxa,phenoData=pd)
64 
+		} else {
65 
+			newObj = newMRexperiment(newMat,featureData=taxa)
66 
+		}
67 
+		warning("\n\nThe output here are aggregated (normalized?) counts.\n
68 
+			Check default parameters for all metagenomeSeq functions so as not to renormalize.")
69 
+		return(newObj)
70 
+	}
50 71 
 }
51 72 
 #' @rdname aggregateByTaxonomy
52 73 
 #' @export
53 
-aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000){
54 
-    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl)
74 
+aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000,out='MRexperiment'){
75 
+	aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl,out=out)
55 76 
 }
56 77 
\ No newline at end of file
Browse code

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

Commit information:

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 1 changed files
R/aggregateByTaxonomy.R
History View file @ a94b8b0
... ... 
@@ -12,6 +12,7 @@
12 12 
 #' @param norm Whether to aggregate normalized counts or not.
13 13 
 #' @param log Whether or not to log2 transform the counts - if MRexperiment object.
14 14 
 #' @param aggfun Aggregation function.
15 
+#' @param sl scaling value, default is 1000.
15 16 
 #' @return An aggregated count matrix.
16 17 
 #' @aliases aggTax
17 18 
 #' @rdname aggregateByTaxonomy
... ... 
@@ -21,9 +22,9 @@
21 22 
 #' # not run
22 23 
 #' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
23 24 
 #'
24 
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums){
25 
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000){
25 26 
 	if(class(obj)=="MRexperiment"){
26 
-		mat = MRcounts(obj,norm=norm,log=log)
27 
+		mat = MRcounts(obj,norm=norm,log=log,sl=sl)
27 28 
     } else {
28 29 
 		stop("Object needs to be a MRexperiment object. If it's a matrix, see aggregateM.")
29 30 
     }
... ... 
@@ -49,6 +50,6 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun
49 50 
 }
50 51 
 #' @rdname aggregateByTaxonomy
51 52 
 #' @export
52 
-aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums){
53 
-    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun)
53 
+aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums,sl=1000){
54 
+    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun,sl=sl)
54 55 
 }
55 56 
\ No newline at end of file
Browse code

Updated fitPA,aggTax and added fitMeta and fitDO

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@85736 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 23/01/2014 04:33:54
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ b327ef5
... ... 
@@ -10,6 +10,7 @@
10 10 
 #' @param lvl featureData column name from the MRexperiment object.
11 11 
 #' @param alternate Use the rowname for undefined OTUs instead of aggregating to "no_match".
12 12 
 #' @param norm Whether to aggregate normalized counts or not.
13 
+#' @param log Whether or not to log2 transform the counts - if MRexperiment object.
13 14 
 #' @param aggfun Aggregation function.
14 15 
 #' @return An aggregated count matrix.
15 16 
 #' @aliases aggTax
... ... 
@@ -20,9 +21,9 @@
20 21 
 #' # not run
21 22 
 #' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
22 23 
 #'
23 
-aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,aggfun = colSums){
24 
+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums){
24 25 
 	if(class(obj)=="MRexperiment"){
25 
-		mat = MRcounts(obj,norm=norm,log=FALSE)
26 
+		mat = MRcounts(obj,norm=norm,log=log)
26 27 
     } else {
27 28 
 		stop("Object needs to be a MRexperiment object. If it's a matrix, see aggregateM.")
28 29 
     }
... ... 
@@ -48,6 +49,6 @@ aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,aggfun = colSums
48 49 
 }
49 50 
 #' @rdname aggregateByTaxonomy
50 51 
 #' @export
51 
-aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,aggfun = colSums){
52 
-    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,aggfun = aggfun)
52 
+aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,log=FALSE,aggfun = colSums){
53 
+    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,log=log,aggfun = aggfun)
53 54 
 }
54 55 
\ No newline at end of file
Browse code

Updated vignette, manual pages, minor changes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84540 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 14/12/2013 00:02:50
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 2d031e1
... ... 
@@ -3,12 +3,12 @@
3 3 
 #'
4 4 
 #' Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a
5 5 
 #' MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts
6 
-#' to the desired level by with the aggfun function (default colSums). Possible aggfun alternatives
6 
+#' to the desired level using the aggfun function (default colSums). Possible aggfun alternatives
7 7 
 #' include colMeans and colMedians.
8 8 
 #'
9 9 
 #' @param obj A MRexperiment object.
10 10 
 #' @param lvl featureData column name from the MRexperiment object.
11 
-#' @param alternatelabel Use the rowname for undefined OTUs instead of aggregating to others.
11 
+#' @param alternate Use the rowname for undefined OTUs instead of aggregating to "no_match".
12 12 
 #' @param norm Whether to aggregate normalized counts or not.
13 13 
 #' @param aggfun Aggregation function.
14 14 
 #' @return An aggregated count matrix.
Browse code

many minor updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84391 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 12/12/2013 19:16:19
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 679d906
... ... 
@@ -8,6 +8,7 @@
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 #'
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 #' @param obj A MRexperiment object.
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 #' @param lvl featureData column name from the MRexperiment object.
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+#' @param alternatelabel Use the rowname for undefined OTUs instead of aggregating to others.
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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.
... ... 
@@ -19,14 +20,22 @@
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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,norm=TRUE,aggfun = colSums){
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+aggregateByTaxonomy<-function(obj,lvl,alternate=FALSE,norm=TRUE,aggfun = colSums){
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 	if(class(obj)=="MRexperiment"){
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 		mat = MRcounts(obj,norm=norm,log=FALSE)
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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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-	levels = fData(obj)[,lvl]
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+	levels = as.character(fData(obj)[,lvl])
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+    nafeatures = is.na(levels)
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+    if(length(nafeatures)>0){
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+        if(alternate==FALSE){
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+            levels[nafeatures] = "no_match"
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+        } else {
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+            levels[nafeatures] = paste("OTU_",rownames(obj)[nafeatures],sep="")
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+        }
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+    }
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 	grps = split(seq_along(levels),levels)
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 	newMat = array(NA,dim=c(length(grps),ncol(obj)))
... ... 
@@ -39,6 +48,6 @@ aggregateByTaxonomy<-function(obj,lvl,norm=TRUE,aggfun = colSums){
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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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+aggTax<-function(obj,lvl,alternate=FALSE,norm=TRUE,aggfun = colSums){
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+    aggregateByTaxonomy(obj,lvl,alternate=alternate,norm=norm,aggfun = aggfun)
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 }
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\ No newline at end of file
Browse code

updated tabs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84100 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 10/12/2013 00:15:08
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ e7c6515
... ... 
@@ -20,10 +20,10 @@
20 20 
 #' # aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)
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 #'
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 aggregateByTaxonomy<-function(obj,lvl,norm=TRUE,aggfun = colSums){
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-    if(class(obj)=="MRexperiment"){
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-        mat = MRcounts(obj,norm=norm,log=FALSE)
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+	if(class(obj)=="MRexperiment"){
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+		mat = MRcounts(obj,norm=norm,log=FALSE)
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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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+		stop("Object needs to be a MRexperiment object. If it's a matrix, see aggregateM.")
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     }
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 	levels = fData(obj)[,lvl]
Browse code

aggregateByTaxonomy/aggTax

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
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 42eba9b
... ... 
@@ -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
... ... 
@@ -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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 #'
... ... 
@@ -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
Browse code

modified some functions to allow matrices, added aggregateByTaxonomy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@84090 bc3139a8-67e5-0310-9ffc-ced21a209358

Joseph Paulson authored on 09/12/2013 23:32:36
Showing 1 changed files
R/aggregateByTaxonomy.R
History View file @ 700b534
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,37 @@
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+#' 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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+#'
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+#' @param obj A MRexperiment object.
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+#' @param lvl featureData column name from the MRexperiment object.
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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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+#' @export
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+#' @examples
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+#'
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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,norm=TRUE,aggfun = colSums){
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+    if(class(obj)=="MRexperiment"){
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+        mat = MRcounts(obj,norm=norm,log=FALSE)
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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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+
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+	levels = fData(obj)[,lvl]
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+	grps = split(seq_along(levels),levels)
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+
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+	newMat = array(NA,dim=c(length(grps),ncol(obj)))
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+	for(i in 1:length(grps)){
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+		newMat[i,] = aggfun(mat[grps[[i]],,drop=FALSE])
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+	}
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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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