Rarmec-package {Rarmec}R Documentation

A simple R interface to query ARMeC

Description

Set of functions to query ARMeC directly from the data analysis process - This is why it is in R! This is a first version and would probably improvements.

Details

Package: Rarmec
Type: Package
Version: 1.0
Date: 2007-09-18
License: GPL version 2.

Author(s)

David Enot

Examples

### Real example using Brachypodium from the FIEmspro package
library(Rarmec)
library(FIEmspro)
library(gplots) ### used in ar.corplot

### Select classes 1 and 2
data(abr1)
dat <- abr1$pos[,110:1000]
l=which(abr1$fact$class==1 | abr1$fact$class==2)
y   <- factor(abr1$fact$class[l])        
x   <- preproc(dat[l,],y, method=c("log10","TICnorm"))  

#### Use randomForest to rank variables
res=fs.rf(x,y,ntree=2000)
#### Select variables with importance score >0.003
lvar=names(which(res$stats>0.003))

#### who are they?
print(lvar)

#### Let's retrieve all possible solutions
## measured adducts is enough for the time being
all.sol<-ar.getlist(lvar,type="meas")

#### Let's dump them in a CSV file for Excel manipulation
write.table(all.sol,"tmp-allsolutions.csv",row.names=FALSE,sep=",")

#### Perform cluster analysis and  plot clustering analysis result
hc<-ar.clust(x,lvar,method="complete")

#### plot overall correlation matrix
## Not run: ar.corplot(hc,x)

#### Retrieve candidates for those adducts have been measured
### Dissimilarity is set to 0.3 to form the clusters
cl.res=ar.splitcl(hc,all.sol,x,h=0.3)

#### Output in the console only nominal masses in each cluster
ar.writecl(cl.res,icl = NULL, cor.mat = FALSE, armec.mat = FALSE)

#### Output in the console guesses for cluster 1 and 2 except the pathway
ar.writecl(cl.res,icl = c(1,2), cor.mat = FALSE, 
   armec.mat = TRUE, path=FALSE)

#### Output in the console guesses for cluster 1 with correlation matrices
## but no pathway information
ar.writecl(cl.res,icl = 1, cor.mat = TRUE, armec.mat = TRUE, path=FALSE)

#### Dump everything in file="tmp-ex-armec.csv"
ar.writecl(cl.res,file="tmp-ex-armec.csv")


[Package Rarmec version 1.0 Index]