impute {ptairMS} | R Documentation

## 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)

[Package ptairMS version 1.0.1 Index]