alignSamples {ptairMS} | R Documentation

## Alignment between samples

### Description

`AlignSamples` performs alignment between samples (i.e. the matching of variables between the peak lists within the `ptrSet` object) by using a kernel gaussian density (Delabriere et al, 2017). This function returns an `ExpressionSet`, which contains the matrix of peak intensities, the sample metadata (borrowed from the input ptrSet) and the variable metadata which contains the peak intensities in the background. Two filters may be applied to:

- keep only variables with a significant higher intensity in the expirations compared to the background (i.e., a p-value less than `pValGreaterThres`) for at least `fracExp`

- keep only variables which are detected in more than `fracGroup` percent of the samples (or `group`)

If you do not want to apply those filters, set `fracGroup` to 0 and `pValGreaterThres` to 1.

### Usage

    alignSamples(
      X,
      ppmGroup = 70,
      fracGroup = 0.8,
      group = NULL,
      fracExp = 0.3,
      pValGreaterThres = 0.001,
      pValLessThres = 0,
      quantiUnit = c("ppb", "ncps", "cps")[1],
      bgCorrected = TRUE,
      dmzGroup = 0.001
    )

    ## S4 method for signature 'ptrSet'
    alignSamples(
      X,
      ppmGroup = 70,
      fracGroup = 0.8,
      group = NULL,
      fracExp = 0.3,
      pValGreaterThres = 0.001,
      pValLessThres = 0,
      quantiUnit = c("ppb", "ncps", "cps")[1],
      bgCorrected = TRUE,
      dmzGroup = 0.001
    )

### Arguments

`X` | ptrSet already processed by the `detectPeak` function
`ppmGroup` | ppm maximal width for an mz group
`fracGroup` | only variables present in `fracGroup` percent of at least one `group` will be kept (if 0 the filter is not applied)
`group` | character: sampleMetadata data column name. If `NULL`, variables not present in `fracGroup` percent of samples will be deleted. Else, variables not present in `fracGroup` percent in in at least one group group will be removed.
`fracExp` | fraction of samples which must have their p-value less than `pValGreaterThres` and `pValLessThres`
`pValGreaterThres` | threshold of the p-value for the unilateral testing that quantification (in cps) of expiration points are greater than the intensities in the background.
`pValLessThres` | threshold of the p-value for the unilateral testing that quantification (in cps) of expiration points are less than the intensities of the background.
`quantiUnit` | ppb, ncps or cps
`bgCorrected` | logical: should the peak table contain the background corrected values?
`dmzGroup` | minimum mz width to be used for grouping the features (required for low masses)

### Value

an `ExpressionSet` (Biobase object)

### References

Delabriere et al., 2017

### 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,mzNominal=c(21,60,79))
    eset <- alignSamples(exhaledPtrset,pValGreaterThres=0.05)
    Biobase::exprs(eset)
    Biobase::fData(eset)
    Biobase::pData(eset)

[Package ptairMS version 1.2.0 Index]