impute: Imputes the missing values

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

Imputes the missing values

Description

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).

Usage

impute(eSet, ptrSet, parallelize = FALSE, nbCores = 2)

Arguments

eSet	ExpressionSet returned by the alignSamples function
ptrSet	ptrSet-class object processed by the detectPeak function
parallelize	boolean. If TRUE, the loop over all files will be parallelized
nbCores	number of clusters to use for parallel computation.

Value

the same ExpressionSet as in input, with the imputed missing values in the assayData slot

Examples

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)

camilleroquencourt/ptairMS documentation built on April 24, 2024, 9:03 p.m.