FormatPeakList: Format Peak List
In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

Description Usage Arguments Value Author(s) See Also Examples

This function formats the CAMERA output to a usable format for OptiLCMS.

FormatPeakList(
  mSet,
  annParams,
  filtIso = TRUE,
  filtAdducts = FALSE,
  missPercent = 0.75
)

`mSet`	The mSet object generated by the PerformPeakAnnotation function.
`annParams`	The object created using the SetAnnotationParam function, containing user's specified or default parameters for downstream raw MS data pre-processing.
`filtIso`	Logical, filter out all isotopes except for `[M]`+ for positive ion mode and `[M]`- for negative ion mode. By default it is set to true.
`filtAdducts`	Logical, filter out all adducts except `[M+H]`+ for positive ion more and `[M-H]`- for negative ion mode. By default it is set to false.
`missPercent`	Numeric, specify the threshold to remove features missing in X\ that are missing from 50\ when there are two groups.

will return a mSet object with all result table formatted

Jasmine Chong jasmine.chong@mail.mcgill.ca, and Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

ExecutePlan and PerformPeakProfiling for the whole pipeline.

data(mSet);
newPath <- dir(system.file("mzData", package = "mtbls2"),
               full.names = TRUE, recursive = TRUE)[c(10, 11, 12)]
mSet <- updateRawSpectraPath(mSet, newPath);
annParams <- SetAnnotationParam(polarity = 'positive',
                                mz_abs_add = 0.035);

## Perform peak annotation with newly deinfed annParams
# mSet <- PerformPeakAnnotation(mSet = mSet,
#                               annotaParam = annParams,
#                               ncore =1)
## Format the PeakList
mSet <- FormatPeakList(mSet = mSet,
                       annParams,
                       filtIso =FALSE,
                       filtAdducts = FALSE,
                       missPercent = 1)