get.clusters: get.clusters
In stuchly/MetaMass: Tools for Mass Spectrometry data meta-analysis

Description Usage Arguments Details Value Examples

View source: R/AnnoMass.R

retrieves cluster data.frame from AnnoMass object

1	get.clusters(AM,rID=1)

`AM`	AnnoMass object. Result of function `analyze.MSfile`
`rID`	integer. Which annotation should be used to the comparison (see annotation.component argument in `analyze.MSfile`)

assigned_location scheme: Cytoplasm : (Cyt + CS (cytoskeleton)+proteasome ) >=51% Subcategory: cytoskeleton if more than 30% of markers in cytoplasm category is cytosleketon

Ribosome (no subcategory) >=51%

Membrane: PM (Plasma membrane) + ER (endoplasmic reticulum)+Golgi+Mitochondrion + lysosomes + ensodomes >=51% Subcategory: Most dominant count.

Nucleus: Nucleus + Nucleolus Subcategory: Nucleolus if more than 25% of nuclear markers are Nucleolus,

data.frame. One line per each cluster with cluster info.

main_component - most abundant component in the cluster purity_main_component - ration of main_component in the cluster Nb_main_component - number of annotation suporting the most abundant component assigned_location - annotation of cluster with respect predefined scheme (see details)

other columns - ratio of other components etc

file1<-system.file("extdata","Bileck.txt",package="MetaMass")
file2<-system.file("extdata","Andreyev.txt",package="MetaMass")
file1
file2
res<-analyze.MSfile(MSfile=c(file1,file2),Metadata=c("Christoforou","Rodriguez"),markers=c(3,4,5,6,7))

head(get.clusters(res,rID=1)) #clusters annotation with respect to the 1st annotation.component (3rd column in AnnotationFile)