Commit information:
Commit id: 91095e5380cc1cc8e62af3850af012809a8c93b3
cleaning up ssPermAnalysis
Committed by: nosson
Author Name: nosson
Commit date: 2015-02-03 16:29:10 -0500
Author date: 2015-02-03 16:29:10 -0500
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@99013 bc3139a8-67e5-0310-9ffc-ced21a209358
Joseph Paulson authored on 03/02/2015 21:29:20
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: metagenomeSeq |
| 2 | 2 |
Title: Statistical analysis for sparse high-throughput sequencing |
| 3 |
-Version: 1.9.22 |
|
| 4 |
-Date: 2015-2-1 |
|
| 3 |
+Version: 1.9.23 |
|
| 4 |
+Date: 2015-2-3 |
|
| 5 | 5 |
Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada |
| 6 | 6 |
Bravo |
| 7 | 7 |
Maintainer: Joseph N. Paulson <jpaulson@umiacs.umd.edu> |
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 |
-version 1.9.xx (2014) |
|
| 1 |
+version 1.9.xx (2015) |
|
| 2 | 2 |
+ Added flexibility in formula choice for fitTimeSeries |
| 3 |
+ + Added readability in ssPermAnalysis |
|
| 3 | 4 |
+ Added fitTimeSeries vignette |
| 4 | 5 |
+ Removed interactiveDisplay to namespace - moved to suggests |
| 5 | 6 |
+ Fixed ordering of MRtable,MRfulltable first four columns |
| ... | ... |
@@ -140,6 +140,7 @@ ssPerm <- function(df,B) {
|
| 140 | 140 |
ssPermAnalysis <- function(data,formula,permList,intTimes,timePoints,include=c("class", "time:class"),...){
|
| 141 | 141 |
resPerm=matrix(NA, length(permList), nrow(intTimes)) |
| 142 | 142 |
permData=data |
| 143 |
+ case = data.frame(time=timePoints, class=factor(levels(data$class)[2])) |
|
| 143 | 144 |
for (j in 1:length(permList)){
|
| 144 | 145 |
|
| 145 | 146 |
permData$class = permList[[j]] |
| ... | ... |
@@ -149,9 +150,8 @@ ssPermAnalysis <- function(data,formula,permList,intTimes,timePoints,include=c("
|
| 149 | 150 |
} else{
|
| 150 | 151 |
permModel = gss::ssanova(abundance ~ time * class,data=permData,...) |
| 151 | 152 |
} |
| 152 |
- permFit = cbind(timePoints, (2*predict(permModel,data.frame(time=timePoints, class=factor(1)),#abs |
|
| 153 |
- include=include, se=TRUE)$fit)) |
|
| 154 | 153 |
|
| 154 |
+ permFit = cbind(timePoints, (2*predict(permModel,case,include=include, se=TRUE)$fit)) |
|
| 155 | 155 |
for (i in 1:nrow(intTimes)){
|
| 156 | 156 |
permArea=permFit[which(permFit[,1]==intTimes[i,1]) : which(permFit[,1]==intTimes[i, 2]), ] |
| 157 | 157 |
resPerm[j, i]=metagenomeSeq::trapz(x=permArea[,1], y=permArea[,2]) |
| ... | ... |
@@ -367,7 +367,7 @@ fitTimeSeries <- function(obj,formula,feature,class,time,id,method=c("ssanova"),
|
| 367 | 367 |
lvl=NULL,include=c("class", "time:class"),C=0,B=1000,
|
| 368 | 368 |
norm=TRUE,log=TRUE,sl=1000,...) {
|
| 369 | 369 |
if(method=="ssanova"){
|
| 370 |
- if(requireNamespace(gss)){
|
|
| 370 |
+ if(requireNamespace("gss")){
|
|
| 371 | 371 |
if(missing(formula)){
|
| 372 | 372 |
res = fitSSTimeSeries(obj=obj,feature=feature,class=class,time=time,id=id, |
| 373 | 373 |
lvl=lvl,C=C,B=B,norm=norm,log=log,sl=sl,include=include,...) |