get.data: get.data

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

Description

retrieves MS data.frame merged with Annotation from AnnoMass object

Usage

get.data(AM,annotation=TRUE,data.only=FALSE,out=FALSE)

Arguments

AM	AnnoMass object. Result of function analyze.MSfile
annotation	if the annotation should be merged with data
data.only	only data (numerical) columns, protein ID and cluster membership is returned
out	the table in the same format as in output_table txtx file is returned
fulltext	only with out=TRUE; fullText annoations from data(full_text_annotation) columns are added

Value

data.frame. One line per protein.

Examples

file1<-system.file("extdata","Rodriguez.txt",package="MetaMass")
file2<-system.file("extdata","Carvalho.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.data(res))
head(get.data(res,annotation=FALSE,data.only=TRUE))

stuchly/MetaMass documentation built on Nov. 14, 2019, 10:58 p.m.