harvestMS2: harvestMS2
In crmclean/ms2sweeper: Finding and Retreiving Best Posible MS2 Spectra

Description Usage Arguments Value

View source: R/harvestMs2s.R

This function connects all MS2 scans belonging to a single feature within a single data sample. It returns the sweeperObj with a slot for the parent ions and a slot for the merged MS2s filled up. It also does a 13C correction of the MS2s if a 13C peak is detected within the parent ion's scan.

1 2	harvestMS2(sweeperObj, ppm = 5, rtError = 15, isoWindow = 2, cores = 3, clearData = TRUE, mzDiff = 0.5)

`sweeperObj`	- object containing all MS2 data that will be mined.
`ppm`	- Error window for features.
`rtError`	- Time window to check for matches in rt betwee parent ions from XCMS and those from the MS2 fragment table.
`isoWindow`	- isolation window for MS2s
`cores`	- number of cores to use during harvest function.
`clearData`	- Boolean. Deletes raw data from sweepersObj. Good to reduce amount of memory taken up by sweeperObj.
`mzDiff`	- mz error window used to group peaks from spectra together. that belong to the same features but come in different scans.