SRMService-class: R access to Bibliospec File
In protViz/SRMService: Report Quantitative Mass Spectrometry Data

Description Details Fields Methods Examples

This class implements an R referenz class for BiblioSpec generated sqlite files and can return the data contained as data.frames or as list of tandem mass spectra peptide assignments objects (psm).

The function performs a SQL query on the SQLite

dbfile: database file location

getMatchingIntensities(): get matrix with intensities, where nr of NAs in row < maxNA
getNrNAs(light = FALSE): show nr of NA's for heavy (defalt) or light transitions
getTransitionIntensities(maxNA, light = FALSE): get matrix with intensities, where nr of NAs in row < maxNA
maxNAHeavy(max): set maximum of na's heavy row
maxNALight(max): set maximum of na's in light row
plotCommonTransitions(light = FALSE): Shows transitions which occure in heavy and light
plotQValues(): show q value distribution for peak groups

if(0){
library(SRMService)
tmp <- "D:/Dropbox/DataAnalysis/p1930_NAGI/"
allData <- read.csv( file=file.path(tmp,"data/longFormat.txt"),row.names = 1)
head(allData)
data <-allData
pool=2
data <-allData[allData$pool==pool,]
head(data)
srms <- SRMService(data,qvalue=0.05)
SRMService$methods()
srms$maxNAHeavy()
SRMService$fields()
head(srms$piw)

srms$plotQValues()
srms$plotTransitions()
srms$plotTransitions(light=TRUE)

srms$getNrNAs()
srms$getNrNAs(light=TRUE)
srms$maxNAHeavy()
srms$maxNALight()
srms$maxNAHeavy(80)
srms$maxNALight(80)
srms$plotCommonTransitions()
srms$plotCommonTransitions(light=TRUE)
tmp <-srms$getLHLog2FoldChange(maxNA = 20)
srms$maxNAFC()
resH <- srms$plotCommonTransitions()
dim(resH)
resL <-srms$plotCommonTransitions(light=TRUE)
dim(resL)
resAll <- srms$getMatchingIntensities()
dim(resAll$light)

tmpH <- srms$getTransitionIntensities()$data
tmpL <- srms$getTransitionIntensities(light=TRUE)$data

dim(tmpL)
transitionTable<-srms$getLHLog2FoldChange()
trans2 <- transitionTable$removeDecorrelated()

}