FormatPeakList: Format Peak List

Description Usage Arguments Value Author(s) See Also Examples

View source: R/Perform_functions.R

Description

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

Usage

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

Arguments

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.

Value

will return a mSet object with all result table formatted

Author(s)

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

See Also

ExecutePlan and PerformPeakProfiling for the whole pipeline.

Examples

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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)

xia-lab/OptiLCMS documentation built on Sept. 6, 2021, 12:36 a.m.