impute {ptairMS} | R Documentation |
Imputes missing values by returning back to the raw data and fitting the peak shape function on the noise (or on the residuals signals if peaks have already been detected).
impute(eSet, ptrSet, parallelize = FALSE, nbCores = 2)
eSet |
ExpressionSet returned by the |
ptrSet |
|
parallelize |
boolean. If |
nbCores |
number of clusters to use for parallel computation. |
the same ExpressionSet as in input, with the imputed missing values in the assayData slot
library(ptairData) dirRaw <- system.file("extdata/exhaledAir", package = "ptairData") exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset", mzCalibRef = c(21.022, 60.0525), fracMaxTIC = 0.7, saveDir = NULL ) exhaledPtrset<-detectPeak(exhaledPtrset,mz=c(21,52)) eSet <- alignSamples(exhaledPtrset,pValGreaterThres=0.05,fracGroup=0) Biobase::exprs(eSet) eSet <- impute(eSet,exhaledPtrset) Biobase::exprs(eSet)